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Sivakumar P, Vaishnavi V, Gayatri K, Satheesh GR, Siddiqi I. Improved validation of protein interactions using bicistronic BiFC (Bi2FC). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1047-1054. [PMID: 39100877 PMCID: PMC11291819 DOI: 10.1007/s12298-024-01477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/10/2024] [Accepted: 06/22/2024] [Indexed: 08/06/2024]
Abstract
Refolding based Bimolecular Fluorescence Complementation (BiFC) has emerged as an important in vivo technique to identify protein interactions. Significant improvements have been made to enhance the detection capacities of BiFC, however less attention has been paid to the detection of expression levels of proteins. Here we demonstrate development and validation of an improved method to identify protein interactions that incorporates an expression control based on bicistronic expression of the protein of interest and a fluorescent protein separated by a self-cleaving peptide. This method gives robust identification of positive interactions and more reliably identifies absence of interactions. We also show an earlier identified non-interacting pair in yeast two-hybrid (Y2H) to be interacting in vivo. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01477-y.
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Affiliation(s)
- Prakash Sivakumar
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Vijayaraj Vaishnavi
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
| | - Kothuri Gayatri
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
| | - Gayathri R. Satheesh
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
| | - Imran Siddiqi
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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2
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Tang X, Ren Q, Yan X, Zhang R, Liu L, Han Q, Zheng X, Qi Y, Song H, Zhang Y. Boosting genome editing in plants with single transcript unit surrogate reporter systems. PLANT COMMUNICATIONS 2024; 5:100921. [PMID: 38616491 PMCID: PMC11211634 DOI: 10.1016/j.xplc.2024.100921] [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: 01/02/2024] [Revised: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
CRISPR-Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement. However, the challenge of low editing activity complicates the identification of editing events. In this study, we introduce multiple single transcript unit surrogate reporter (STU-SR) systems to enhance the selection of genome-edited plants. These systems use the same single guide RNAs designed for endogenous genes to edit reporter genes, establishing a direct link between reporter gene editing activity and that of endogenous genes. Various strategies are used to restore functional reporter genes after genome editing, including efficient single-strand annealing (SSA) for homologous recombination in STU-SR-SSA systems. STU-SR-base editor systems leverage base editing to reinstate the start codon, enriching C-to-T and A-to-G base editing events. Our results showcase the effectiveness of these STU-SR systems in enhancing genome editing events in the monocot rice, encompassing Cas9 nuclease-based targeted mutagenesis, cytosine base editing, and adenine base editing. The systems exhibit compatibility with Cas9 variants, such as the PAM-less SpRY, and are shown to boost genome editing in Brassica oleracea, a dicot vegetable crop. In summary, we have developed highly efficient and versatile STU-SR systems for enrichment of genome-edited plants.
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Affiliation(s)
- Xu Tang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qiurong Ren
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; School of Synbiology, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xiaodan Yan
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Rui Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Li Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qinqin Han
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Xuelian Zheng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Hongyuan Song
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China.
| | - Yong Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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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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4
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Zhao S, Luo J, Tang M, Zhang C, Song M, Wu G, Yan X. Analysis of the Candidate Genes and Underlying Molecular Mechanism of P198, an RNAi-Related Dwarf and Sterile Line. Int J Mol Sci 2023; 25:174. [PMID: 38203344 PMCID: PMC10778984 DOI: 10.3390/ijms25010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotypes. In this study, a dwarf and sterile line named P198 was screened from the Brassica napus (B. napus) RNAi library. Three different methods confirmed that eight copies of T-DNA are present in the P198 genome. However, only four insertion positions were identified in three chromosomes using fusion primer and nested integrated polymerase chain reaction. Therefore, the T-DNA insertion sites and copy number were further investigated using Oxford Nanopore Technologies (ONT) sequencing, and it was found that at least seven copies of T-DNA were inserted into three insertion sites. Based on the obtained T-DNA insertion sites and hairpin RNA (hpRNA) cassette sequences, three candidate genes related to the P198 phenotype were identified. Furthermore, the potential differentially expressed genes and pathways involved in the dwarfism and sterility phenotype of P198 were investigated by RNA-seq. These results demonstrate the advantage of applying ONT sequencing to investigate the molecular characteristics of transgenic lines and expand our understanding of the complex molecular mechanism of dwarfism and male sterility in B. napus.
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Affiliation(s)
- Shengbo Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junling Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Min Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Miaoying Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohong Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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Bi M, Wang Z, Cheng K, Cui Y, He Y, Ma J, Qi M. Construction of transcription factor mutagenesis population in tomato using a pooled CRISPR/Cas9 plasmid library. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108094. [PMID: 37995578 DOI: 10.1016/j.plaphy.2023.108094] [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: 05/18/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
Adequate mutant materials are the prerequisite for conducting gene function research or screening novel functional genes in plants. The strategy of constructing a large-scale mutant population using the pooled CRISPR/Cas9-sgRNA library has been implemented in several crops. However, the effective application of this CRISPR/Cas9 large-scale screening strategy to tomato remains to be attempted. Here, we identified 990 transcription factors in the tomato genome, designed and synthesized a CRISPR/Cas9 plasmid library containing 4379 sgRNAs. Using this pooled library, 487 T0 positive plants were obtained, among which 92 plants harbored a single sgRNA sequence, targeting 65 different transcription factors, with a mutation rate of 23%. In the T0 mutant population, the occurrence of homozygous and biallelic mutations was observed at higher frequencies. Additionally, the utilization of a small-scale CRISPR/Cas9 library targeting 30 transcription factors could enhance the efficacy of single sgRNA recognition in positive plants, increasing it from 19% to 42%. Phenotypic characterization of several mutants identified from the mutant population demonstrated the utility of our CRISPR/Cas9 mutant library. Taken together, our study offers insights into the implementation and optimization of CRISPR/Cas9-mediated large-scale knockout library in tomato.
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Affiliation(s)
- Mengxi Bi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Zhijun Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Keyan Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Yiqing Cui
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Yi He
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Jian Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China.
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Tran HT, Schramm C, Huynh MM, Shavrukov Y, Stangoulis JCR, Jenkins CLD, Anderson PA. An accurate, reliable, and universal qPCR method to identify homozygous single insert T-DNA with the example of transgenic rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1221790. [PMID: 37900763 PMCID: PMC10600460 DOI: 10.3389/fpls.2023.1221790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023]
Abstract
Early determination of transgenic plants that are homozygous for a single locus T-DNA insert is highly desirable in most fundamental and applied transgenic research. This study aimed to build on an accurate, rapid, and reliable quantitative real-time PCR (qPCR) method to fast-track the development of multiple homozygous transgenic rice lines in the T1 generation, with low copy number to single T-DNA insert for further analyses. Here, a well-established qPCR protocol, based on the OsSBE4 reference gene and the nos terminator, was optimized in the transgenic Japonica rice cultivar Nipponbare, to distinguish homozygous single-insert plants with 100% accuracy. This method was successfully adapted to transgenic Indica rice plants carrying three different T-DNAs, without any modifications to quickly develop homozygous rice plants in the T1 generation. The accuracy of this qPCR method when applied to transgenic Indica rice approached 100% in 12 putative transgenic lines. Moreover, this protocol also successfully detected homozygous single-locus T-DNA transgenic rice plants with two-transgene T-DNAs, a feature likely to become more popular in future transgenic research. The assay was developed utilizing universal primers targeting common sequence elements of gene cassettes (the nos terminator). This assay could therefore be applied to other transgenic plants carrying the nos terminator. All procedures described here use standardized qPCR reaction conditions and relatively inexpensive dyes, such as SYBR Green, thus the qPCR method could be cost-effective and suitable for lower budget laboratories that are involved in rice transgenic research.
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Affiliation(s)
- Hai Thanh Tran
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | | | | | | | | | - Peter A. Anderson
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Characterization of Agrobacterium-mediated co-transformation events in rice using green and red fluorescent proteins. Mol Biol Rep 2022; 49:9613-9622. [PMID: 36040546 DOI: 10.1007/s11033-022-07864-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/11/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Biotechnologists seeking to develop marker-free transgenic plants have established co-transformation methods. For co-transformation using mixed Agrobacterium strains, the mix ratio of Agrobacterium strains and selection scheme may influence co-transformation frequency. This study used fluorescent GFP and RFP markers to compose different selection schemes for observation of the selective dynamics of transformed rice cells and to investigate the factors affecting co-transformation efficiency. METHODS AND RESULTS We utilized GFP and RFP markers in co-transformation and tested the combinations of an antibiotic-selectable vector (pGFP-HPT) and a single RFP vector (pRFP) and of two antibiotic-selectable vectors (pGFP-HPT and pRFP-HPT) in rice. The pGFP-HPT/pRFP combination resulted in 70.9% to 81.2% of co-transformation frequencies while lower frequencies (56.6% on average) were obtained with the pGFP-HPT/pRFP-HPT combination. Based on GFP/RFP segregation patterns, 55% of the pGFP-HPT/pRFP co-transformants contained unlinked T-DNAs and segregated single RFP progeny, which simulated the selection process of marker-free transgenic plants that carry an actual gene of interest. Transgene expression levels in the rice lines varied as revealed by RT-PCR, and tandem-linked T-DNAs were detected in co-transformants, suggesting that transgene expression might be affected by duplicated T-DNA structures. CONCLUSION Co-transformation via mixed Agrobacterium strains is feasible, and approximately 55% of the pGFP-HPT/pRFP co-transformants contained unlinked T-DNAs and segregated single RFP progeny. The pGFP-HPT/pRFP and the pGFP-HPT/pRFP-HPT vector combinations showed distinctive selective dynamics of transformed rice cells, suggesting that co-transformation efficiency depends on both vector system and selection scheme.
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8
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Hata T, Takada N, Hayakawa C, Kazama M, Uchikoba T, Tachikawa M, Matsuo M, Satoh S, Obokata J. De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome. PLoS One 2021; 16:e0252674. [PMID: 34111139 PMCID: PMC8191969 DOI: 10.1371/journal.pone.0252674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/19/2021] [Indexed: 01/16/2023] Open
Abstract
The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related chromatin marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. A comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription concomitant with local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism by which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome.
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Affiliation(s)
- Takayuki Hata
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
| | - Naoto Takada
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Chihiro Hayakawa
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Mei Kazama
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Tomohiro Uchikoba
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Makoto Tachikawa
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
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9
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Sashidhar N, Harloff HJ, Potgieter L, Jung C. Gene editing of three BnITPK genes in tetraploid oilseed rape leads to significant reduction of phytic acid in seeds. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2241-2250. [PMID: 32191373 PMCID: PMC7589381 DOI: 10.1111/pbi.13380] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/07/2020] [Accepted: 02/28/2020] [Indexed: 05/20/2023]
Abstract
Commercialization of Brassica napus. L (oilseed rape) meal as protein diet is gaining more attention due to its well-balanced amino acid and protein contents. Phytic acid (PA) is a major source of phosphorus in plants but is considered as anti-nutritive for monogastric animals including humans due to its adverse effects on essential mineral absorption. The undigested PA causes eutrophication, which potentially threatens aquatic life. PA accounts to 2-5% in mature seeds of oilseed rape and is synthesized by complex pathways involving multiple enzymes. Breeding polyploids for recessive traits is challenging as gene functions are encoded by several paralogs. Gene redundancy often requires to knock out several gene copies to study their underlying effects. Therefore, we adopted CRISPR-Cas9 mutagenesis to knock out three functional paralogs of BnITPK. We obtained low PA mutants with an increase of free phosphorus in the canola grade spring cultivar Haydn. These mutants could mark an important milestone in rapeseed breeding with an increase in protein value and no adverse effects on oil contents.
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Affiliation(s)
- Niharika Sashidhar
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
| | - Hans J. Harloff
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
| | - Lizel Potgieter
- Environmental GenomicsBotanical InstituteChristian‐Albrechts‐University of KielKielGermany
- Environmental GenomicsMax‐Planck‐Institute for Evolutionary BiologyPlönGermany
| | - Christian Jung
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
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Ruiz Y, Ramos PL, Soto J, Rodríguez M, Carlos N, Reyes A, Callard D, Sánchez Y, Pujol M, Fuentes A. The M4 insulator, the TM2 matrix attachment region, and the double copy of the heavy chain gene contribute to the enhanced accumulation of the PHB-01 antibody in tobacco plants. Transgenic Res 2020; 29:171-186. [PMID: 31919795 DOI: 10.1007/s11248-019-00187-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/31/2019] [Indexed: 11/24/2022]
Abstract
The expression of recombinant proteins in plants is a valuable alternative to bioreactors using mammalian cell systems. Ease of scaling, and their inability to host human pathogens, enhance the use of plants to generate complex therapeutic products such as monoclonal antibodies. However, stably transformed plants expressing antibodies normally have a poor accumulation of these proteins that probably arise from the negative positional effects of their flanking chromatin. The induction of boundaries between the transgenes and the surrounding DNA using matrix attachment regions (MAR) and insulator elements may minimize these effects. With the PHB-01 antibody as a model, we demonstrated that the insertion of DNA elements, the TM2 (MAR) and M4 insulator, flanking the transcriptional cassettes that encode the light and heavy chains of the PHB-01 antibody, increased the protein accumulation that remained stable in the first plant progeny. The M4 insulator had a stronger effect than the TM2, with over a twofold increase compared to the standard construction. This effect was probably associated with an enhancer-promoter interference. Moreover, transgenic plants harboring two transcriptional units encoding for the PHB-01 heavy chain combined with both TM2 and M4 elements enhanced the accumulation of the antibody. In summary, the M4 combined with a double transcriptional unit of the heavy chain may be a suitable strategy for potentiating PHB-01 production in tobacco plants.
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Affiliation(s)
- Yoslaine Ruiz
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba.
| | - Pedro Luis Ramos
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
- Department of Phytopathology and Plant Biochemistry, Instituto Biologico, São Paulo, Brazil
| | - Jeny Soto
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
- Comparative Pathology Department, University of Miami, Miami, USA
| | - Meilyn Rodríguez
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Natacha Carlos
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Aneisi Reyes
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Danay Callard
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Yadira Sánchez
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Merardo Pujol
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Alejandro Fuentes
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba.
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11
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Pereman I, Melamed-Bessudo C, Dahan-Meir T, Herz E, Elbaum M, Levy AA. Single Molecule Imaging of T-DNA Intermediates Following Agrobacterium tumefaciens Infection in Nicotiana benthamiana. Int J Mol Sci 2019; 20:ijms20246209. [PMID: 31835367 PMCID: PMC6940882 DOI: 10.3390/ijms20246209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/27/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
Plant transformation mediated by Agrobacterium tumefaciens is a well-studied phenomenon in which a bacterial DNA fragment (T-DNA), is transferred to the host plant cell, as a single strand, via type IV secretion system and has the potential to reach the nucleus and to be integrated into its genome. While Agrobacterium-mediated transformation has been widely used for laboratory-research and in breeding, the time-course of its journey from the bacterium to the nucleus, the conversion from single- to double-strand intermediates and several aspects of the integration in the genome remain obscure. In this study, we sought to follow T-DNA infection directly using single-molecule live imaging. To this end, we applied the LacO-LacI imaging system in Nicotiana benthamiana, which enabled us to identify double-stranded T-DNA (dsT-DNA) molecules as fluorescent foci. Using confocal microscopy, we detected progressive accumulation of dsT-DNA foci in the nucleus, starting 23 h after transfection and reaching an average of 5.4 and 8 foci per nucleus at 48 and 72 h post-infection, respectively. A time-course diffusion analysis of the T-DNA foci has demonstrated their spatial confinement.
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Affiliation(s)
- Idan Pereman
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
- Migal, Galilee Research Institute, Kiryat Shmona 11016, Israel
- Correspondence: (I.P.); (M.E); (A.A.L.)
| | - Cathy Melamed-Bessudo
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Dahan-Meir
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elad Herz
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael Elbaum
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot 76100, Israel
- Correspondence: (I.P.); (M.E); (A.A.L.)
| | - Avraham A. Levy
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
- Correspondence: (I.P.); (M.E); (A.A.L.)
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12
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Yun JY, Kim ST, Kim SG, Kim JS. A zero-background CRISPR binary vector system for construction of sgRNA libraries in plant functional genomics applications. PLANT BIOTECHNOLOGY REPORTS 2019; 13:543-551. [DOI: 10.1007/s11816-019-00567-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/17/2019] [Indexed: 08/30/2023]
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13
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Palaci J, Virdi V, Depicker A. Transformation strategies for stable expression of complex hetero-multimeric proteins like secretory immunoglobulin A in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1760-1769. [PMID: 30801876 PMCID: PMC6686127 DOI: 10.1111/pbi.13098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
Plant expression systems have proven to be exceptional in producing high-value complex polymeric proteins such as secretory IgAs (SIgAs). However, polymeric protein production requires the expression of multiple genes, which can be transformed as single or multiple T-DNA units to generate stable transgenic plant lines. Here, we evaluated four strategies to stably transform multiple genes and to obtain high expression of all components. Using the in-seed expression of a simplified secretory IgA (sSIgA) as a reference molecule, we conclude that it is better to spread the genes over two T-DNAs than to contain them in a single T-DNA, because of the presence of homologous recombination events and gene silencing. These T-DNAs can be cotransformed to obtain transgenic plants in one transformation step. However, if time permits, more transformants with high production levels of the polymeric protein can be obtained either by sequential transformation or by in-parallel transformation followed by crossing of transformants independently selected for excellent expression of the genes in each T-DNA.
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Affiliation(s)
- Jorge Palaci
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- VIB Center for Plant Systems BiologyGentBelgium
| | - Vikram Virdi
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- VIB Center for Plant Systems BiologyGentBelgium
- Department of Biochemistry and MicrobiologyGhent UniversityGentBelgium
- VIB Center for Medical BiotechnologyGentBelgium
| | - Ann Depicker
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- VIB Center for Plant Systems BiologyGentBelgium
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14
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Anand A, Wu E, Li Z, TeRonde S, Arling M, Lenderts B, Mutti JS, Gordon‐Kamm W, Jones TJ, Chilcoat ND. High efficiency Agrobacterium-mediated site-specific gene integration in maize utilizing the FLP-FRT recombination system. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1636-1645. [PMID: 30706638 PMCID: PMC6662307 DOI: 10.1111/pbi.13089] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/23/2019] [Accepted: 01/27/2019] [Indexed: 05/20/2023]
Abstract
An efficient Agrobacterium-mediated site-specific integration (SSI) technology using the flipase/flipase recognition target (FLP/FRT) system in elite maize inbred lines is described. The system allows precise integration of a single copy of a donor DNA flanked by heterologous FRT sites into a predefined recombinant target line (RTL) containing the corresponding heterologous FRT sites. A promoter-trap system consisting of a pre-integrated promoter followed by an FRT site enables efficient selection of events. The efficiency of this system is dependent on several factors including Agrobacterium tumefaciens strain, expression of morphogenic genes Babyboom (Bbm) and Wuschel2 (Wus2) and choice of heterologous FRT pairs. Of the Agrobacterium strains tested, strain AGL1 resulted in higher transformation frequency than strain LBA4404 THY- (0.27% vs. 0.05%; per cent of infected embryos producing events). The addition of morphogenic genes increased transformation frequency (2.65% in AGL1; 0.65% in LBA4404 THY-). Following further optimization, including the choice of FRT pairs, a method was developed that achieved 19%-22.5% transformation frequency. Importantly, >50% of T0 transformants contain the desired full-length site-specific insertion. The frequencies reported here establish a new benchmark for generating targeted quality events compatible with commercial product development.
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Affiliation(s)
- Ajith Anand
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Emily Wu
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Zhi Li
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Sue TeRonde
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Maren Arling
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Brian Lenderts
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Jasdeep S. Mutti
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | | | - Todd J. Jones
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
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15
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Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR. The complex architecture and epigenomic impact of plant T-DNA insertions. PLoS Genet 2019; 15:e1007819. [PMID: 30657772 PMCID: PMC6338467 DOI: 10.1371/journal.pgen.1007819] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/07/2018] [Indexed: 12/17/2022] Open
Abstract
The bacterium Agrobacterium tumefaciens has been the workhorse in plant genome engineering. Customized replacement of native tumor-inducing (Ti) plasmid elements enabled insertion of a sequence of interest called Transfer-DNA (T-DNA) into any plant genome. Although these transfer mechanisms are well understood, detailed understanding of structure and epigenomic status of insertion events was limited by current technologies. Here we applied two single-molecule technologies and analyzed Arabidopsis thaliana lines from three widely used T-DNA insertion collections (SALK, SAIL and WISC). Optical maps for four randomly selected T-DNA lines revealed between one and seven insertions/rearrangements, and the length of individual insertions from 27 to 236 kilobases. De novo nanopore sequencing-based assemblies for two segregating lines partially resolved T-DNA structures and revealed multiple translocations and exchange of chromosome arm ends. For the current TAIR10 reference genome, nanopore contigs corrected 83% of non-centromeric misassemblies. The unprecedented contiguous nucleotide-level resolution enabled an in-depth study of the epigenome at T-DNA insertion sites. SALK_059379 line T-DNA insertions were enriched for 24nt small interfering RNAs (siRNA) and dense cytosine DNA methylation, resulting in transgene silencing via the RNA-directed DNA methylation pathway. In contrast, SAIL_232 line T-DNA insertions are predominantly targeted by 21/22nt siRNAs, with DNA methylation and silencing limited to a reporter, but not the resistance gene. Additionally, we profiled the H3K4me3, H3K27me3 and H2A.Z chromatin environments around T-DNA insertions using ChIP-seq in SALK_059379, SAIL_232 and five additional T-DNA lines. We discovered various effect s ranging from complete loss of chromatin marks to the de novo incorporation of H2A.Z and trimethylation of H3K4 and H3K27 around the T-DNA integration sites. This study provides new insights into the structural impact of inserting foreign fragments into plant genomes and demonstrates the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes. Our routine ability to add or alter genes in plant genomes using transgenesis has proven to be a game changer to plant sciences. Transgenics not only enables the study of gene function but also allows the development of modern crop plants without the unwanted genetic baggage coming from natural crossing. A major tool to create transgenics is the Agrobacterium system which naturally shuttles and integrates pieces of foreign DNA into its host genome. While the position and number of integrations was relatively easy to track, molecular tools never allowed to see the integrated piece of DNA within a single “picture”. Here we have utilized state-of-the-art DNA sequencing technology to capture the size and structure of multiple DNA insertion events in a plant genome. We discovered that insertion of the anticipated DNA fragment occurred as multiple concatenated full and partial fragments that led in some cases to intra- and interchromosomal rearrangements. Our analysis of the epigenetic landscapes showed variable effects from silencing of the integrated foreign DNA to alterations of chromatin marks and thus chromatin structure and functionality.
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Affiliation(s)
- Florian Jupe
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Angeline C. Rivkin
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Todd P. Michael
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Mark Zander
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | | | - Justin P. Sandoval
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Joseph R. Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- * E-mail:
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16
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Hayta S, Smedley MA, Demir SU, Blundell R, Hinchliffe A, Atkinson N, Harwood WA. An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat ( Triticum aestivum L.). PLANT METHODS 2019; 15:121. [PMID: 31673278 PMCID: PMC6815027 DOI: 10.1186/s13007-019-0503-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/14/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Despite wheat being a worldwide staple, it is still considered the most difficult to transform out of the main cereal crops. Therefore, for the wheat research community, a freely available and effective wheat transformation system is still greatly needed. RESULTS We have developed and optimised a reproducible Agrobacterium-mediated transformation system for the spring wheat cv 'Fielder' that yields transformation efficiencies of up to 25%. We report on some of the important factors that influence transformation efficiencies. In particular, these include donor plant health, stage of the donor material, pre-treatment by centrifugation, vector type and selection cassette. Transgene copy number data for independent plants regenerated from the same original immature embryo suggests that multiple transgenic events arise from single immature embryos, therefore, actual efficiencies might be even higher than those reported. CONCLUSION We reported here a high-throughput, highly efficient and repeatable transformation system for wheat and this system has been used successfully to introduce genes of interest, for RNAi, over-expression and for CRISPR-Cas9 based genome editing.
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Affiliation(s)
- Sadiye Hayta
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH UK
| | - Mark A. Smedley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH UK
| | - Selcen U. Demir
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH UK
| | - Robert Blundell
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH UK
| | - Alison Hinchliffe
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH UK
| | - Nicola Atkinson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH UK
| | - Wendy A. Harwood
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH UK
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17
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Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. eLife 2018. [PMID: 29521624 PMCID: PMC5922974 DOI: 10.7554/elife.32110] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi. The fungus Rhodosporidium toruloides can grow on substances extracted from plant matter that is inedible to humans such as corn stalks, wood pulp, and grasses. Under some growth conditions, the fungus can accumulate massive stores of hydrocarbon-rich fats and pigments. A community of scientists and engineers has begun genetically modifying R. toruloides to convert these naturally produced fats and pigments into fuels, chemicals and medicines. These could form sustainable replacements for products made from petroleum or harvested from threatened animal and plant species. Fungi, plants, animals and other eukaryotes store fat in specialized compartments called lipid droplets. The genes that control the metabolism – the production, use and storage – of fat in lipid bodies have been studied in certain eukaryotes, including species of yeast. However, R. toruloides is only distantly related to the most well-studied of these species. This means that we cannot be certain that a gene will play the same role in R. toruloides as in those species. To assemble the most comprehensive list possible of the genes in R. toruloides that affect the production, use, or storage of fat in lipid bodies, Coradetti, Pinel et al. constructed a population of hundreds of thousands of mutant fungal strains, each with its own unique DNA ‘barcode’. The effects that mutations in over 6,000 genes had on growth and fat accumulation in these fungi were measured simultaneously in several experiments. This general approach is not new, but technical limitations had, until now, restricted its use in fungi to a few species. Coradetti, Pinel et al. identified hundreds of genes that affected the ability of R. toruloides to metabolise fat. Many of these genes were related to genes with known roles in fat metabolism in other eukaryotes. Other genes are involved in different cell processes, such as the recycling of waste products in the cell. Their identification adds weight to the view that the links between these cellular processes and fat metabolism are deep and widespread amongst eukaryotes. Finally, some of the genes identified by Coradetti, Pinel et al. are not closely related to any well-studied genes. Further study of these genes could help us to understand why R. toruloides can accumulate much larger amounts of fat than most other fungi. The methods developed by Coradetti, Pinel et al. should be possible to implement in many species of fungi. As a result these techniques may eventually contribute to the development of new treatments for human fungal diseases, the protection of important food crops, and a deeper understanding of the roles various fungi play in the broader ecosystem.
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Affiliation(s)
| | - Dominic Pinel
- Energy Biosciences Institute, Berkeley, United States
| | | | - Masakazu Ito
- Energy Biosciences Institute, Berkeley, United States
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, United States.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, United States
| | - Ya-Fang Cheng
- Energy Biosciences Institute, Berkeley, United States
| | - Stefan Bauer
- Energy Biosciences Institute, Berkeley, United States
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel B Brem
- The Buck Institute for Research on Aging, Novato, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Adam P Arkin
- Energy Biosciences Institute, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Jeffrey M Skerker
- Energy Biosciences Institute, Berkeley, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
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18
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Advancing Agrobacterium-Based Crop Transformation and Genome Modification Technology for Agricultural Biotechnology. Curr Top Microbiol Immunol 2018; 418:489-507. [PMID: 29959543 DOI: 10.1007/82_2018_97] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites. A majority of these deficiencies have now been addressed by improving the frequency of quality events, developing genotype-independent transformation capability in maize, developing an Agrobacterium-based site-specific integration technology for precise gene targeting, and adopting Agrobacterium-delivered CRISPR-Cas genes for gene editing. These improved transformation technologies are discussed in detail in this chapter.
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19
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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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20
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Hwang HH, Yu M, Lai EM. Agrobacterium-mediated plant transformation: biology and applications. THE ARABIDOPSIS BOOK 2017; 15:e0186. [PMID: 31068763 PMCID: PMC6501860 DOI: 10.1199/tab.0186] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant genetic transformation heavily relies on the bacterial pathogen Agrobacterium tumefaciens as a powerful tool to deliver genes of interest into a host plant. Inside the plant nucleus, the transferred DNA is capable of integrating into the plant genome for inheritance to the next generation (i.e. stable transformation). Alternatively, the foreign DNA can transiently remain in the nucleus without integrating into the genome but still be transcribed to produce desirable gene products (i.e. transient transformation). From the discovery of A. tumefaciens to its wide application in plant biotechnology, numerous aspects of the interaction between A. tumefaciens and plants have been elucidated. This article aims to provide a comprehensive review of the biology and the applications of Agrobacterium-mediated plant transformation, which may be useful for both microbiologists and plant biologists who desire a better understanding of plant transformation, protein expression in plants, and plant-microbe interaction.
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Affiliation(s)
- Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, 402
| | - Manda Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, 115
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, 115
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21
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An Insight into T-DNA Integration Events in Medicago sativa. Int J Mol Sci 2017; 18:ijms18091951. [PMID: 28895894 PMCID: PMC5618600 DOI: 10.3390/ijms18091951] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/24/2017] [Accepted: 09/06/2017] [Indexed: 11/16/2022] Open
Abstract
The molecular mechanisms of transferred DNA (T-DNA) integration into the plant genome are still not completely understood. A large number of integration events have been analyzed in different species, shedding light on the molecular mechanisms involved, and on the frequent transfer of vector sequences outside the T-DNA borders, the so-called vector backbone (VB) sequences. In this work, we characterized 46 transgenic alfalfa (Medicago sativa L.) plants (events), generated in previous works, for the presence of VB tracts, and sequenced several T-DNA/genomic DNA (gDNA) junctions. We observed that about 29% of the transgenic events contained VB sequences, within the range reported in other species. Sequence analysis of the T-DNA/gDNA junctions evidenced larger deletions at LBs compared to RBs and insertions probably originated by different integration mechanisms. Overall, our findings in alfalfa are consistent with those in other plant species. This work extends the knowledge on the molecular events of T-DNA integration and can help to design better transformation protocols for alfalfa.
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22
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van Tol N, Rolloos M, Pinas JE, Henkel CV, Augustijn D, Hooykaas PJJ, van der Zaal BJ. Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors. PLoS One 2017; 12:e0174236. [PMID: 28358915 PMCID: PMC5373528 DOI: 10.1371/journal.pone.0174236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
The rapidly growing world population has a greatly increasing demand for plant biomass, thus creating a great interest in the development of methods to enhance the growth and biomass accumulation of crop species. In this study, we used zinc finger artificial transcription factor (ZF-ATF)-mediated genome interrogation to manipulate the growth characteristics and biomass of Arabidopsis plants. We describe the construction of two collections of Arabidopsis lines expressing fusions of three zinc fingers (3F) to the transcriptional repressor motif EAR (3F-EAR) or the transcriptional activator VP16 (3F-VP16), and the characterization of their growth characteristics. In total, six different 3F-ATF lines with a consistent increase in rosette surface area (RSA) of up to 55% were isolated. For two lines we demonstrated that 3F-ATF constructs function as dominant in trans acting causative agents for an increase in RSA and biomass, and for five larger plant lines we have investigated 3F-ATF induced transcriptomic changes. Our results indicate that genome interrogation can be used as a powerful tool for the manipulation of plant growth and biomass and that it might supply novel cues for the discovery of genes and pathways involved in these properties.
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Affiliation(s)
- Niels van Tol
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
- BioSolar Cells, Wageningen, The Netherlands
| | - Martijn Rolloos
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Johan E. Pinas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Christiaan V. Henkel
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Dieuwertje Augustijn
- Leiden Institute of Chemistry, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Paul J. J. Hooykaas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Bert J. van der Zaal
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
- * E-mail:
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23
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Char SN, Neelakandan AK, Nahampun H, Frame B, Main M, Spalding MH, Becraft PW, Meyers BC, Walbot V, Wang K, Yang B. An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:257-268. [PMID: 27510362 PMCID: PMC5259581 DOI: 10.1111/pbi.12611] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/29/2016] [Accepted: 08/04/2016] [Indexed: 05/18/2023]
Abstract
CRISPR/Cas9 is a powerful genome editing tool in many organisms, including a number of monocots and dicots. Although the design and application of CRISPR/Cas9 is simpler compared to other nuclease-based genome editing tools, optimization requires the consideration of the DNA delivery and tissue regeneration methods for a particular species to achieve accuracy and efficiency. Here, we describe a public sector system, ISU Maize CRISPR, utilizing Agrobacterium-delivered CRISPR/Cas9 for high-frequency targeted mutagenesis in maize. This system consists of an Escherichia coli cloning vector and an Agrobacterium binary vector. It can be used to clone up to four guide RNAs for single or multiplex gene targeting. We evaluated this system for its mutagenesis frequency and heritability using four maize genes in two duplicated pairs: Argonaute 18 (ZmAgo18a and ZmAgo18b) and dihydroflavonol 4-reductase or anthocyaninless genes (a1 and a4). T0 transgenic events carrying mono- or diallelic mutations of one locus and various combinations of allelic mutations of two loci occurred at rates over 70% mutants per transgenic events in both Hi-II and B104 genotypes. Through genetic segregation, null segregants carrying only the desired mutant alleles without the CRISPR transgene could be generated in T1 progeny. Inheritance of an active CRISPR/Cas9 transgene leads to additional target-specific mutations in subsequent generations. Duplex infection of immature embryos by mixing two individual Agrobacterium strains harbouring different Cas9/gRNA modules can be performed for improved cost efficiency. Together, the findings demonstrate that the ISU Maize CRISPR platform is an effective and robust tool to targeted mutagenesis in maize.
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Affiliation(s)
- Si Nian Char
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| | | | | | - Bronwyn Frame
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Marcy Main
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Martin H. Spalding
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| | - Philip W. Becraft
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| | | | | | - Kan Wang
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Bing Yang
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
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24
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van Kregten M, de Pater S, Romeijn R, van Schendel R, Hooykaas PJJ, Tijsterman M. T-DNA integration in plants results from polymerase-θ-mediated DNA repair. NATURE PLANTS 2016; 2:16164. [PMID: 27797358 DOI: 10.1038/nplants.2016.164] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/27/2016] [Indexed: 05/22/2023]
Abstract
Agrobacterium tumefaciens is a pathogenic bacterium, which transforms plants by transferring a discrete segment of its DNA, the T-DNA, to plant cells. The T-DNA then integrates into the plant genome. T-DNA biotechnology is widely exploited in the genetic engineering of model plants and crops. However, the molecular mechanism underlying T-DNA integration remains unknown1. Here we demonstrate that in Arabidopsis thaliana T-DNA integration critically depends on polymerase theta (Pol θ). We find that TEBICHI/POLQ mutant plants (which have mutated Pol θ), although susceptible to Agrobacterium infection, are resistant to T-DNA integration. Characterization of >10,000 T-DNA-plant genome junctions reveals a distinct signature of Pol θ action and also indicates that 3' end capture at genomic breaks is the prevalent mechanism of T-DNA integration. The primer-template switching ability of Pol θ can explain the molecular patchwork known as filler DNA that is frequently observed at sites of integration. T-DNA integration signatures in other plant species closely resemble those of Arabidopsis, suggesting that Pol-θ-mediated integration is evolutionarily conserved. Thus, Pol θ provides the mechanism for T-DNA random integration into the plant genome, demonstrating a potential to disrupt random integration so as to improve the quality and biosafety of plant transgenesis.
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Affiliation(s)
- Maartje van Kregten
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Sylvia de Pater
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Ron Romeijn
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Paul J J Hooykaas
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
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25
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Ko M, Cho JH, Seo HH, Lee HH, Kang HY, Nguyen TS, Soh HC, Kim YS, Kim JI. Constitutive expression of a fungus-inducible carboxylesterase improves disease resistance in transgenic pepper plants. PLANTA 2016; 244:379-92. [PMID: 27074836 DOI: 10.1007/s00425-016-2514-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/30/2016] [Indexed: 05/10/2023]
Abstract
Resistance against anthracnose fungi was enhanced in transgenic pepper plants that accumulated high levels of a carboxylesterase, PepEST in anthracnose-susceptible fruits, with a concurrent induction of antioxidant enzymes and SA-dependent PR proteins. A pepper esterase gene (PepEST) is highly expressed during the incompatible interaction between ripe fruits of pepper (Capsicum annuum L.) and a hemibiotrophic anthracnose fungus (Colletotrichum gloeosporioides). In this study, we found that exogenous application of recombinant PepEST protein on the surface of the unripe pepper fruits led to a potentiated state for disease resistance in the fruits, including generation of hydrogen peroxide and expression of pathogenesis-related (PR) genes that encode mostly small proteins with antimicrobial activity. To elucidate the role of PepEST in plant defense, we further developed transgenic pepper plants overexpressing PepEST under the control of CaMV 35S promoter. Molecular analysis confirmed the establishment of three independent transgenic lines carrying single copy of transgenes. The level of PepEST protein was estimated to be approximately 0.002 % of total soluble protein in transgenic fruits. In response to the anthracnose fungus, the transgenic fruits displayed higher expression of PR genes, PR3, PR5, PR10, and PepThi, than non-transgenic control fruits did. Moreover, immunolocalization results showed concurrent localization of ascorbate peroxidase (APX) and PR3 proteins, along with the PepEST protein, in the infected region of transgenic fruits. Disease rate analysis revealed significantly low occurrence of anthracnose disease in the transgenic fruits, approximately 30 % of that in non-transgenic fruits. Furthermore, the transgenic plants also exhibited resistance against C. acutatum and C. coccodes. Collectively, our results suggest that overexpression of PepEST in pepper confers enhanced resistance against the anthracnose fungi by activating the defense signaling pathways.
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Affiliation(s)
- Moonkyung Ko
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Jung Hyun Cho
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Hyo-Hyoun Seo
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Hyun-Hwa Lee
- Department of Biology, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Ha-Young Kang
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Thai Son Nguyen
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Hyun Cheol Soh
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Young Soon Kim
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea.
| | - Jeong-Il Kim
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea.
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26
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Dietz-Pfeilstetter A, Arndt N, Manske U. Effects of a petunia scaffold/matrix attachment region on copy number dependency and stability of transgene expression in Nicotiana tabacum. Transgenic Res 2016; 25:149-62. [PMID: 26732611 DOI: 10.1007/s11248-015-9924-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/17/2015] [Indexed: 01/28/2023]
Abstract
Transgenes in genetically modified plants are often not reliably expressed during development or in subsequent generations. Transcriptional gene silencing (TGS) as well as post-transcriptional gene silencing (PTGS) have been shown to occur in transgenic plants depending on integration pattern, copy number and integration site. In an effort to reduce position effects, to prevent read-through transcription and to provide a more accessible chromatin structure, a P35S-ß-glucuronidase (P35S-gus) transgene flanked by a scaffold/matrix attachment region from petunia (Petun-SAR), was introduced in Nicotiana tabacum plants by Agrobacterium tumefaciens mediated transformation. It was found that Petun-SAR mediates enhanced expression and copy number dependency up to 2 gene copies, but did not prevent gene silencing in transformants with multiple and rearranged gene copies. However, in contrast to the non-SAR transformants where silencing was irreversible and proceeded during long-term vegetative propagation and in progeny plants, gus expression in Petun-SAR plants was re-established in the course of development. Gene silencing was not necessarily accompanied by DNA methylation, while the gus transgene could still be expressed despite considerable CG methylation within the coding region.
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Affiliation(s)
- Antje Dietz-Pfeilstetter
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104, Braunschweig, Germany.
| | - Nicola Arndt
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Ulrike Manske
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104, Braunschweig, Germany
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27
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Inagaki S, Henry IM, Lieberman MC, Comai L. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture. PLoS One 2015; 10:e0139672. [PMID: 26445462 PMCID: PMC4596565 DOI: 10.1371/journal.pone.0139672] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/16/2015] [Indexed: 01/19/2023] Open
Abstract
Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.
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Affiliation(s)
- Soichi Inagaki
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
- Department of Integrative Genetics, National Institute of Genetics, Mishima, Japan
| | - Isabelle M. Henry
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
| | - Meric C. Lieberman
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
| | - Luca Comai
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
- * E-mail:
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28
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Germline-transmitted genome editing in Arabidopsis thaliana Using TAL-effector-nucleases. PLoS One 2015; 10:e0121056. [PMID: 25822541 PMCID: PMC4378910 DOI: 10.1371/journal.pone.0121056] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/29/2015] [Indexed: 11/19/2022] Open
Abstract
Transcription activator-like effector nucleases (TALENs) are custom-made bi-partite endonucleases that have recently been developed and applied for genome engineering in a wide variety of organisms. However, they have been only scarcely used in plants, especially for germline-modification. Here we report the efficient creation of small, germline-transmitted deletions in Arabidopsis thaliana via TALENs that were delivered by stably integrated transgenes. Using meristem specific promoters to drive expression of two TALEN arms directed at the CLV3 coding sequence, we observed very high phenotype frequencies in the T2 generation. In some instances, full CLV3 loss-of-function was already observed in the T1 generation, suggesting that transgenic delivery of TALENs can cause highly efficient genome modification. In contrast, constitutive TALEN expression in the shoot apical meristem (SAM) did not cause additional phenotypes and genome re-sequencing confirmed little off-target effects, demonstrating exquisite target specificity.
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29
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Chen K, Dorlhac de Borne F, Szegedi E, Otten L. Deep sequencing of the ancestral tobacco species Nicotiana tomentosiformis reveals multiple T-DNA inserts and a complex evolutionary history of natural transformation in the genus Nicotiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:669-82. [PMID: 25219519 DOI: 10.1111/tpj.12661] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 07/30/2014] [Accepted: 08/29/2014] [Indexed: 05/21/2023]
Abstract
Nicotiana species carry cellular T-DNA sequences (cT-DNAs), acquired by Agrobacterium-mediated transformation. We characterized the cT-DNA sequences of the ancestral Nicotiana tabacum species Nicotiana tomentosiformis by deep sequencing. N. tomentosiformis contains four cT-DNA inserts derived from different Agrobacterium strains. Each has an incomplete inverted-repeat structure. TA is similar to part of the Agrobacterium rhizogenes 1724 mikimopine-type T-DNA, but has unusual orf14 and mis genes. TB carries a 1724 mikimopine-type orf14-mis fragment and a mannopine-agropine synthesis region (mas2-mas1-ags). The mas2' gene codes for an active enzyme. TC is similar to the left part of the A. rhizogenes A4 T-DNA, but also carries octopine synthase-like (ocl) and c-like genes normally found in A. tumefaciens. TD shows a complex rearrangement of T-DNA fragments similar to the right end of the A4 TL-DNA, and including an orf14-like gene and a gene with unknown function, orf511. The TA, TB, TC and TD insertion sites were identified by alignment with N. tabacum and Nicotiana sylvestris sequences. The divergence values for the TA, TB, TC and TD repeats provide an estimate for their relative introduction times. A large deletion has occurred in the central part of the N. tabacum cv. Basma/Xanthi TA region, and another deletion removed the complete TC region in N. tabacum. Nicotiana otophora lacks TA, TB and TD, but contains TC and another cT-DNA, TE. This analysis, together with that of Nicotiana glauca and other Nicotiana species, indicates multiple sequential insertions of cT-DNAs during the evolution of the genus Nicotiana.
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Affiliation(s)
- Ke Chen
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du C. N. R. S., Rue du Général Zimmer 12, 67084, Strasbourg, France
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30
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Rodrigues RB, Sabat G, Minkoff BB, Burch HL, Nguyen TT, Sussman MR. Expression of a translationally fused TAP-tagged plasma membrane proton pump in Arabidopsis thaliana. Biochemistry 2014; 53:566-78. [PMID: 24397334 PMCID: PMC3985734 DOI: 10.1021/bi401096m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The Arabidopsis thaliana plasma
membrane proton ATPase genes, AHA1 and AHA2, are the two most highly expressed isoforms of an 11 gene family
and are collectively essential for embryo development. We report the
translational fusion of a tandem affinity-purification tag to the
5′ end of the AHA1 open reading frame in a genomic clone. Stable
expression of TAP-tagged AHA1 in Arabidopsis rescues the embryonic lethal phenotype of endogenous double aha1/aha2 knockdowns. Western blots of SDS-PAGE and Blue
Native gels show enrichment of AHA1 in plasma membrane fractions and
indicate a hexameric quaternary structure. TAP-tagged AHA1 rescue
lines exhibited reduced vertical root growth. Analysis of the plasma
membrane and soluble proteomes identified several plasma membrane-localized
proteins with alterred abundance in TAP-tagged AHA1 rescue lines compared
to wild type. Using affinity-purification mass spectrometry, we uniquely
identified two additional AHA isoforms, AHA9 and AHA11, which copurified
with TAP-tagged AHA1. In conclusion, we have generated transgenic Arabidopsis lines in which a TAP-tagged AHA1 transgene
has complemented all essential endogenous AHA1 and AHA2 functions
and have shown that these plants can be used to purify AHA1 protein
and to identify in planta interacting proteins by
mass spectrometry.
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Affiliation(s)
- Rachel B Rodrigues
- Department of Biochemistry, Biotechnology Center, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
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31
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Vermeersch L, De Winne N, Depicker A. Detection and investigation of transitive gene silencing in plants. Methods Mol Biol 2014; 1112:219-241. [PMID: 24478018 DOI: 10.1007/978-1-62703-773-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
RNA-induced post-transcriptional silencing is a common tool in functional gene analysis and its application in crop improvement is widely investigated. However, its specificity might be impaired by off-target silencing as a result of transitivity. Generally transitivity is investigated by the detection of secondary siRNAs; however, these tests fail to demonstrate the siRNA's bioactivity. Here, we describe protocols to detect the occurrence of transitive silencing across an endogene by using a reporter GUS gene. In addition, we provide a setup to test the influence of a sequence of interest present in the primary target on the progression of transitivity.
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Affiliation(s)
- Leen Vermeersch
- Department of Plant Systems Biology, VIB, Ghent University, Ghent, Belgium
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32
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Lampropoulos A, Sutikovic Z, Wenzl C, Maegele I, Lohmann JU, Forner J. GreenGate---a novel, versatile, and efficient cloning system for plant transgenesis. PLoS One 2013; 8:e83043. [PMID: 24376629 PMCID: PMC3869738 DOI: 10.1371/journal.pone.0083043] [Citation(s) in RCA: 285] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 11/08/2013] [Indexed: 12/02/2022] Open
Abstract
Building expression constructs for transgenesis is one of the fundamental day-to-day tasks in modern biology. Traditionally it is based on a multitude of type II restriction endonucleases and T4 DNA ligase. Especially in case of long inserts and applications requiring high-throughput, this approach is limited by the number of available unique restriction sites and the need for designing individual cloning strategies for each project. Several alternative cloning systems have been developed in recent years to overcome these issues, including the type IIS enzyme based Golden Gate technique. Here we introduce our GreenGate system for rapidly assembling plant transformation constructs, which is based on the Golden Gate method. GreenGate cloning is simple and efficient since it uses only one type IIS restriction endonuclease, depends on only six types of insert modules (plant promoter, N-terminal tag, coding sequence, C-terminal tag, plant terminator and plant resistance cassette), but at the same time allows assembling several expression cassettes in one binary destination vector from a collection of pre-cloned building blocks. The system is cheap and reliable and when combined with a library of modules considerably speeds up cloning and transgene stacking for plant transformation.
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Affiliation(s)
- Athanasios Lampropoulos
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Zoran Sutikovic
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Christian Wenzl
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Ira Maegele
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jan U. Lohmann
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Joachim Forner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
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33
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Ghedira R, De Buck S, Van Ex F, Angenon G, Depicker A. T-DNA transfer and T-DNA integration efficiencies upon Arabidopsis thaliana root explant cocultivation and floral dip transformation. PLANTA 2013; 238:1025-1037. [PMID: 23975012 DOI: 10.1007/s00425-013-1948-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 08/09/2013] [Indexed: 06/02/2023]
Abstract
T-DNA transfer and integration frequencies during Agrobacterium-mediated root explant cocultivation and floral dip transformations of Arabidopsis thaliana were analyzed with and without selection for transformation-competent cells. Based on the presence or absence of CRE recombinase activity without or with the CRE T-DNA being integrated, transient expression versus stable transformation was differentiated. During root explant cocultivation, continuous light enhanced the number of plant cells competent for interaction with Agrobacterium and thus the number of transient gene expression events. However, in transformation competent plant cells, continuous light did not further enhance cotransfer or cointegration frequencies. Upon selection for root transformants expressing a first T-DNA, 43-69 % of these transformants showed cotransfer of another non-selected T-DNA in two different light regimes. However, integration of the non-selected cotransferred T-DNA occurred only in 19-46 % of these transformants, indicating that T-DNA integration in regenerating root cells limits the transformation frequencies. After floral dip transformation, transient T-DNA expression without integration could not be detected, while stable T-DNA transformation occurred in 0.5-1.3 % of the T1 seedlings. Upon selection for floral dip transformants with a first T-DNA, 8-34 % of the transformants showed cotransfer of the other non-selected T-DNA and in 93-100 % of them, the T-DNA was also integrated. Therefore, a productive interaction between the agrobacteria and the female gametophyte, rather than the T-DNA integration process, restricts the floral dip transformation frequencies.
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Affiliation(s)
- Rim Ghedira
- Department Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Sylvie De Buck
- Department Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Frédéric Van Ex
- Laboratory of Plant Genetics, Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel (VUB), 1050, Brussel, Belgium
- Bayer CropScience NV, Technologiepark 38, 9052, Ghent, Belgium
| | - Geert Angenon
- Laboratory of Plant Genetics, Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel (VUB), 1050, Brussel, Belgium
| | - Ann Depicker
- Department Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
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34
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De Paepe A, De Buck S, Nolf J, Van Lerberge E, Depicker A. Site-specific T-DNA integration in Arabidopsis thaliana mediated by the combined action of CRE recombinase and ϕC31 integrase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:172-184. [PMID: 23574114 DOI: 10.1111/tpj.12202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 06/02/2023]
Abstract
Random T-DNA integration into the plant host genome can be problematic for a variety of reasons, including potentially variable transgene expression as a result of different integration positions and multiple T-DNA copies, the risk of mutating the host genome and the difficulty of stacking well-defined traits. Therefore, recombination systems have been proposed to integrate the T-DNA at a pre-selected site in the host genome. Here, we demonstrate the capacity of the ϕC31 integrase (INT) for efficient targeted T-DNA integration. Moreover, we show that the iterative site-specific integration system (ISSI), which combines the activities of the CRE recombinase and INT, enables the targeting of genes to a pre-selected site with the concomitant removal of the resident selectable marker. To begin, plants expressing both the CRE and INT recombinase and containing the target attP site were constructed. These plants were supertransformed with a T-DNA vector harboring the loxP site, the attB sites, a selectable marker and an expression cassette encoding a reporter protein. Three out of the 35 transformants obtained (9%) showed transgenerational site-specific integration (SSI) of this T-DNA and removal of the resident selectable marker, as demonstrated by PCR, Southern blot and segregation analysis. In conclusion, our results show the applicability of the ISSI system for precise and targeted Agrobacterium-mediated integration, allowing the serial integration of transgenic DNA sequences in plants.
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Affiliation(s)
- Annelies De Paepe
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sylvie De Buck
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jonah Nolf
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Els Van Lerberge
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ann Depicker
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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Ghedira R, De Buck S, Nolf J, Depicker A. The efficiency of Arabidopsis thaliana floral dip transformation is determined not only by the Agrobacterium strain used but also by the physiology and the ecotype of the dipped plant. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:823-32. [PMID: 23581821 DOI: 10.1094/mpmi-11-12-0267-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
To evaluate the chromosomal background of different Agrobacterium strains on floral dip transformation frequency, eight wild-type Agrobacterium strains, provided by Laboratorium voor Microbiologie Gent (LMG) and classified in different genomic groups, were compared with the commonly used Agrobacterium strains C58C1 Rif(r) (pMP90) and LBA4404 in Arabidopsis thaliana Columbia (Col-0) and C24 ecotypes. The C58C1 Rif(r) chromosomal background in combination with the pMP90 virulence plasmid showed high Col-0 floral dip transformation frequencies (0.76 to 1.57%). LMG201, which is genetically close to the Agrobacterium C58 strain, with the same virulence plasmid showed comparable or even higher transformation frequencies (1.22 to 2.28%), whereas the LBA4404 strain displayed reproducibly lower transformation frequencies (<0.2%). All other tested LMG Agrobacterium chromosomal backgrounds had transformation frequencies between those of the C58C1 Rif(r) (pMP90) and LBA4404 reference strains. None of the strains could transform the C24 ecotype with a frequency higher than 0.1%. Strikingly, all Arabidopsis Col-0 floral dip transformation experiments showed a high transformation variability from plant to plant (even more than 50-fold) within and across the performed biological repeats for all analyzed Agrobacterium strains. Therefore, the physiology of the plant and, probably, the availability of competent flowers to be transformed determine, to a large extent, floral dip transformation frequencies.
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Affiliation(s)
- Rim Ghedira
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
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36
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Liang Z, Tzfira T. In vivo formation of double-stranded T-DNA molecules by T-strand priming. Nat Commun 2013; 4:2253. [PMID: 23963047 DOI: 10.1038/ncomms3253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 07/04/2013] [Indexed: 11/08/2022] Open
Abstract
During plant genetic transformation, Agrobacterium transfers a single-stranded DNA (T-strand) into the host cell. Increasing evidence suggests that double-stranded (ds) T-DNA, converted from T-strands, are potent substrates for integration. Nevertheless, the molecular mechanism governing T-strand conversion to dsT-DNA is unknown. Integrated T-DNA molecules typically exhibit deletions at their 3' end as compared with their 5' end. We hypothesize that this may result from asymmetric polymerization of T-DNA's ends. Here we show that β-glucuronidase (GUS) expression from sense T-strands is more efficient than from antisense T-strands, supporting asymmetric conversion. Co-transfection with two partially complementary, truncated GUS-encoding T-strands results in GUS expression, which suggests functional hybridization of the T-strands via complementary annealing and supports the notion that T-strands can anneal with primers. Indeed, red fluorescent protein (RFP) expression from mutated T-strand can be restored by delivery of synthetic DNA and RNA oligonucleotides with partial wild-type RFP sequence, implying the involvement of plant DNA repair machinery.
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Affiliation(s)
- Zhuobin Liang
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, Michigan 48109, USA
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Da Ines O, White CI. Gene Site-Specific Insertion in Plants. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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38
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Mehrotra S, Goyal V. Evaluation of designer crops for biosafety--a scientist's perspective. Gene 2012; 515:241-8. [PMID: 23266812 DOI: 10.1016/j.gene.2012.12.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/26/2012] [Accepted: 12/04/2012] [Indexed: 01/16/2023]
Abstract
With the advent of transgenic technology, it has become possible to mobilize and express foreign genes into plants and to design crop varieties with better agronomic attributes and adaptability to challenging environmental conditions. Recent advances in transgenic technology have led to concerns about safety of transgenic crops to human and animal health and environment. Biosafety focuses on preventing, minimizing and eliminating risks associated with the research, production, and use of transgenic crops. Food biosafety involves studies of substantial equivalence related to compositional analysis, toxicity and allergenicity. Environmental biosafety involves glasshouse and field trials and study of unintended effects on non-target organisms. Transgenics are characterized at phenotypic and molecular levels for understanding the location of transgene insertion site, ploidy level, copy number, integrated vector sequences, protein expression and stability of the transgene. Various techniques employed for transgene characterization include flow cytometry, southern, northern and western analyses, real-time (qRT) PCR, competitive PCR, FISH, fiber-FISH, DNA micro-arrays, mRNA profiling, 2DE-MS, iTRAQ, FT-MS, NMR, GC-MS, CE-MS and biosensor-based approaches. Evaluation of transgene expression involves the application of integrated phenomics, transcriptomics, proteomics and metabolomics approaches. However, the relevance and application of these approaches may vary in different cases. The elaborate analysis of transgenic crops will facilitate the safety assessment and commercialization of transgenics and lead to global food security for the future.
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Affiliation(s)
- Shweta Mehrotra
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi-110012, India.
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Hensel G, Oleszczuk S, Daghma DES, Zimny J, Melzer M, Kumlehn J. Analysis of T-DNA integration and generative segregation in transgenic winter triticale (x Triticosecale Wittmack). BMC PLANT BIOLOGY 2012; 12:171. [PMID: 23006412 PMCID: PMC3507641 DOI: 10.1186/1471-2229-12-171] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 09/21/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND While the genetic transformation of the major cereal crops has become relatively routine, to date only a few reports were published on transgenic triticale, and robust data on T-DNA integration and segregation have not been available in this species. RESULTS Here, we present a comprehensive analysis of stable transgenic winter triticale cv. Bogo carrying the selectable marker gene HYGROMYCIN PHOSPHOTRANSFERASE (HPT) and a synthetic green fluorescent protein gene (gfp). Progeny of four independent transgenic plants were comprehensively investigated with regard to the number of integrated T-DNA copies, the number of plant genomic integration loci, the integrity and functionality of individual T-DNA copies, as well as the segregation of transgenes in T1 and T2 generations, which also enabled us to identify homozygous transgenic lines. The truncation of some integrated T-DNAs at their left end along with the occurrence of independent segregation of multiple T-DNAs unintendedly resulted in a single-copy segregant that is selectable marker-free and homozygous for the gfp gene. The heritable expression of gfp driven by the maize UBI-1 promoter was demonstrated by confocal laser scanning microscopy. CONCLUSIONS The used transformation method is a valuable tool for the genetic engineering of triticale. Here we show that comprehensive molecular analyses are required for the correct interpretation of phenotypic data collected from the transgenic plants.
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Affiliation(s)
- Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Plant Reproductive Biology, Corrensstr. 3, 06466, Gatersleben, Germany
| | - Sylwia Oleszczuk
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, 05-870, Błonie, Poland
| | - Diaa Eldin S Daghma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Structural Cell Biology, Corrensstr. 3, 06466, Gatersleben, Germany
- National Gene Bank and Genetic Resources, Agriculture Research Center, 12619, Giza, Egypt
| | - Janusz Zimny
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, 05-870, Błonie, Poland
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Structural Cell Biology, Corrensstr. 3, 06466, Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Plant Reproductive Biology, Corrensstr. 3, 06466, Gatersleben, Germany
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Singer K, Shiboleth YM, Li J, Tzfira T. Formation of complex extrachromosomal T-DNA structures in Agrobacterium tumefaciens-infected plants. PLANT PHYSIOLOGY 2012; 160:511-22. [PMID: 22797657 PMCID: PMC3440224 DOI: 10.1104/pp.112.200212] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 07/12/2012] [Indexed: 05/09/2023]
Abstract
Agrobacterium tumefaciens is a unique plant pathogenic bacterium renowned for its ability to transform plants. The integration of transferred DNA (T-DNA) and the formation of complex insertions in the genome of transgenic plants during A. tumefaciens-mediated transformation are still poorly understood. Here, we show that complex extrachromosomal T-DNA structures form in A. tumefaciens-infected plants immediately after infection. Furthermore, these extrachromosomal complex DNA molecules can circularize in planta. We recovered circular T-DNA molecules (T-circles) using a novel plasmid-rescue method. Sequencing analysis of the T-circles revealed patterns similar to the insertion patterns commonly found in transgenic plants. The patterns include illegitimate DNA end joining, T-DNA truncations, T-DNA repeats, binary vector sequences, and other unknown "filler" sequences. Our data suggest that prior to T-DNA integration, a transferred single-stranded T-DNA is converted into a double-stranded form. We propose that termini of linear double-stranded T-DNAs are recognized and repaired by the plant's DNA double-strand break-repair machinery. This can lead to circularization, integration, or the formation of extrachromosomal complex T-DNA structures that subsequently may integrate.
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MESH Headings
- Agrobacterium tumefaciens/pathogenicity
- Ampicillin/pharmacology
- Cloning, Molecular
- DNA End-Joining Repair
- DNA, Bacterial/genetics
- DNA, Circular/genetics
- DNA, Single-Stranded/genetics
- Drug Resistance, Bacterial
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genetic Vectors/genetics
- Plant Diseases/microbiology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Plants, Genetically Modified/microbiology
- Plasmids/genetics
- Sequence Analysis, DNA/methods
- Nicotiana/genetics
- Nicotiana/metabolism
- Nicotiana/microbiology
- Transformation, Genetic
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Affiliation(s)
- Kamy Singer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA.
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Lee S, Su G, Lasserre E, Aghazadeh MA, Murai N. Small high-yielding binary Ti vectors pLSU with co-directional replicons for Agrobacterium tumefaciens-mediated transformation of higher plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 187:49-58. [PMID: 22404832 DOI: 10.1016/j.plantsci.2012.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 05/31/2023]
Abstract
Small high-yielding binary Ti vectors of Agrobacterium tumefaciens were constructed to increase the cloning efficiency and plasmid yield in Escherichia coli and A. tumefaciens for transformation of higher plants. We reduced the size of the binary vector backbone to 4566bp with ColE1 replicon (715bp) for E. coli and VS1 replicon (2654bp) for A. tumefaciens, a bacterial kanamycin resistance gene (999bp), and the T-DNA region (152bp). The binary Ti vectors with the truncated VS1 replicon were stably maintained with more than 98% efficiency in A. tumefaciens without antibiotic selection for 4 days of successive transfers. The transcriptional direction of VS1 replicon can be the same as that of ColE1 replicon (co-directional transcription), or opposite (head-on transcription) as in the case of widely used vectors (pPZP or pCambia). New binary vectors with co-directional transcription yielded in E. coli up to four-fold higher transformation frequency than those with the head-on transcription. In A. tumefaciens the effect of co-directional transcription is still positive in up to 1.8-fold higher transformation frequency than that of head-on transcription. Transformation frequencies of new vectors are over six-fold higher than those of pCambia vector in A. tumefaciens. DNA yields of new vectors were three to five-fold greater than pCambia in E. coli. The proper functions of the new T-DNA borders and new plant selection marker genes were confirmed after A. tumefaciens-mediated transformation of tobacco leaf discs, resulting in virtually all treated leaf discs transformed and induced calli. Genetic analysis of kanamycin resistance trait among the progeny showed that the kanamycin resistance and sensitivity traits were segregated into the 3:1 ratio, indicating that the kanamycin resistance genes were integrated stably into a locus or closely linked loci of the nuclear chromosomal DNA of the primary transgenic tobacco plants and inherited to the second generation.
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Affiliation(s)
- Seokhyun Lee
- Department of Plant Pathology and Crop Physiology, 302 Life Sciences Building, Louisiana State University and LSU Agricultural Center, Baton Rouge, LA 70803-1720, USA
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De Paepe A, De Buck S, Nolf J, Depicker A. High frequency of single-copy T-DNA transformants produced after floral dip in CRE-expressing Arabidopsis plants. Methods Mol Biol 2012; 847:317-333. [PMID: 22351019 DOI: 10.1007/978-1-61779-558-9_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transgenic plants that harbor a single copy of the introduced transgene are preferable to those with multiple transgene copies because multiple T-DNA copies correlate with expression variability and susceptibility to silencing. Especially after the commonly used floral-dip Agrobacterium-mediated transformation method, the frequency of single-copy transformants is low. The CRE/loxP recombinase-based strategy to resolve complex T-DNA loci has proven to be successful to efficiently obtain single-copy T-DNA transformants by directly transforming loxP-containing T-DNA vectors in CRE-expressing Arabidopsis thaliana plants. This chapter describes in detail how to transform three available loxP-containing T-DNA vectors into CRE-producing Arabidopsis C24 plants and subsequently how to analyze the transgenic plants for the T-DNA locus structure.
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Affiliation(s)
- Annelies De Paepe
- Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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43
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De Buck S, Virdi V, De Meyer T, De Wilde K, Piron R, Nolf J, Van Lerberge E, De Paepe A, Depicker A. Production of camel-like antibodies in plants. Methods Mol Biol 2012; 911:305-24. [PMID: 22886260 DOI: 10.1007/978-1-61779-968-6_19] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Transgenic plants for the production of high-value recombinant complex and/or glycosylated proteins are a promising alternative for conventional systems, such as mammalian cells and bacteria. Many groups use plants as production platform for antibodies and antibody fragments. Here, we describe how bivalent camel-like antibodies can be produced in leaves and seeds. Camel-like antibodies are fusions of the antigen-binding domain of heavy chain camel antibodies (VHH) with an Fc fragment of choice. Transient expression in Nicotiana benthamiana leaves allows the production of VHH-Fc antibodies within a few days after the expression plasmid has been obtained. Generation of stable Arabidopsis thaliana transformants allows production of scalable amounts of VHH-Fc antibodies in seeds within a year. Further, we describe how the in planta-produced VHH-Fc antibodies can be quantified by Western blot analysis with Fc-specific antibodies.
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Affiliation(s)
- Sylvie De Buck
- Department of Plant Systems Biology, VIB, Ghent, Belgium
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44
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Yang L, Fu FL, Fu FL, Li WC. [T-DNA integration patterns in transgenic plants mediated by Agrobacterium tumefaciens]. YI CHUAN = HEREDITAS 2011; 33:1327-1334. [PMID: 22207378 DOI: 10.3724/sp.j.1005.2011.01327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genetic transformation mediated by Agrobacterium tumefaciens has been widely applied to research of transgenic plants. As the vector of the exotic genes, the integration patterns of T-DNA fragments affects not only transformation efficiency and stability, but also expression properties of the transgenes. This review summaries the two major patterns and the rules of T-DNA integration in Agrobacterim-mediated transformation, rules of T-DNA mediated by Agrobacterium tumefaciens, as well as research tools for flanking sequence amplification. It is attempted to provide references for researches on transformation and T-DNA integration mutation mediated by Agrobacterium tumefaciens.
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Affiliation(s)
- Lin Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China.
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45
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Gase K, Weinhold A, Bozorov T, Schuck S, Baldwin IT. Efficient screening of transgenic plant lines for ecological research. Mol Ecol Resour 2011; 11:890-902. [PMID: 21518300 DOI: 10.1111/j.1755-0998.2011.03017.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plants stably transformed to manipulate the expression of genes mediating ecological performance have profoundly altered research in plant ecology. Agrobacterium-mediated transformation remains the most effective method of creating plants harbouring a limited number of transgene integrations of low complexity. For ecological/physiological research, the following requirements must be met: (i) the regenerated plants should have the same ploidy level as the corresponding wild-type plant and (ii) contain a single transgene copy in a homozygous state; (iii) the T-DNA must be completely inserted without vector backbone sequence and all its elements functional; and (iv) the integration should not change the phenotype of the plant by interrupting chromosomal genes or by mutations occurring during the regeneration procedure. The screening process to obtain transformed plants that meet the above criteria is costly and time-consuming, and an optimized screening procedure is presented. We developed a flow chart that optimizes the screening process to efficiently select transformed plants for ecological research. It consists of segregational analyses, which select transgenic T₁ and T₂ generation plants with single T-DNA copies that are homozygous. Indispensable molecular genetic tests (flow cytometry, diagnostic PCRs and Southern blotting) are performed at the earliest and most effective times in the screening process. qPCR to quantify changes in transcript accumulation to confirm gene silencing or overexpression is the last step in the selection process. Because we routinely transform the wild tobacco, Nicotiana attenuata, with constructs that silence or ectopically overexpress ecologically relevant genes, the proposed protocol is supported by examples from this system.
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Affiliation(s)
- Klaus Gase
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany
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46
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Nandy S, Srivastava V. Site-specific gene integration in rice genome mediated by the FLP-FRT recombination system. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:713-21. [PMID: 21083801 DOI: 10.1111/j.1467-7652.2010.00577.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant transformation based on random integration of foreign DNA often generates complex integration structures. Precision in the integration process is necessary to ensure the formation of full-length, single-copy integration. Site-specific recombination systems are versatile tools for precise genomic manipulations such as DNA excision, inversion or integration. The yeast FLP-FRT recombination system has been widely used for DNA excision in higher plants. Here, we report the use of FLP-FRT system for efficient targeting of foreign gene into the engineered genomic site in rice. The transgene vector containing a pair of directly oriented FRT sites was introduced by particle bombardment into the cells containing the target locus. FLP activity generated by the co-bombarded FLP gene efficiently separated the transgene construct from the vector-backbone and integrated the backbone-free construct into the target site. Strong FLP activity, derived from the enhanced FLP protein, FLPe, was important for the successful site-specific integration (SSI). The majority of the transgenic events contained a precise integration and expressed the transgene. Interestingly, each transgenic event lacked the co-bombarded FLPe gene, suggesting reversion of the integration structure in the presence of the constitutive FLPe expression. Progeny of the precise transgenic lines inherited the stable SSI locus and expressed the transgene. This work demonstrates the application of FLP-FRT system for site-specific gene integration in plants using rice as a model.
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Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
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47
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Lebedev VG, Schestibratov KA, Shadrina TE, Bulatova IV, Abramochkin DG, Miroshnikov AI. Cotransformation of aspen and birch with three T-DNA regions from two different replicons in one Agrobacterium tumefaciens strain. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410110025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Oltmanns H, Frame B, Lee LY, Johnson S, Li B, Wang K, Gelvin SB. Generation of backbone-free, low transgene copy plants by launching T-DNA from the Agrobacterium chromosome. PLANT PHYSIOLOGY 2010; 152:1158-66. [PMID: 20023148 PMCID: PMC2832237 DOI: 10.1104/pp.109.148585] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 12/13/2009] [Indexed: 05/25/2023]
Abstract
In both applied and basic research, Agrobacterium-mediated transformation is commonly used to introduce genes into plants. We investigated the effect of three Agrobacterium tumefaciens strains and five transferred (T)-DNA origins of replication on transformation frequency, transgene copy number, and the frequency of integration of non-T-DNA portions of the T-DNA-containing vector (backbone) into the genome of Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). Launching T-DNA from the picA locus of the Agrobacterium chromosome increases the frequency of single transgene integration events and almost eliminates the presence of vector backbone sequences in transgenic plants. Along with novel Agrobacterium strains we have developed, our findings are useful for improving the quality of T-DNA integration events.
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Affiliation(s)
| | | | | | | | | | | | - Stanton B. Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907–1392 (H.O., L.-Y.L., S.J., B.L., S.B.G.); Department of Agronomy and Plant Transformation Facility, Iowa State University, Ames, Iowa 50010–1010 (B.F., K.W.)
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49
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Gelvin SB. Plant proteins involved in Agrobacterium-mediated genetic transformation. ANNUAL REVIEW OF PHYTOPATHOLOGY 2010; 48:45-68. [PMID: 20337518 DOI: 10.1146/annurev-phyto-080508-081852] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Agrobacterium species genetically transform plants by transferring a region of plasmid DNA, T-DNA, into host plant cells. The bacteria also transfer several virulence effector proteins. T-DNA and virulence proteins presumably form T-complexes within the plant cell. Super-T-complexes likely also form by interaction of plant-encoded proteins with T-complexes. These protein-nucleic acid complexes traffic through the plant cytoplasm, enter the nucleus, and eventually deliver T-DNA to plant chromatin. Integration of T-DNA into the plant genome establishes a permanent transformation event, permitting stable expression of T-DNA-encoded transgenes. The transformation process is complex and requires participation of numerous plant proteins. This review discusses our current knowledge of plant proteins that contribute to Agrobacterium-mediated transformation, the roles these proteins play in the transformation process, and the modern technologies that have been employed to elucidate the cell biology of transformation.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.
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