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Roushan MR, Shao S, Poledri I, Hooykaas PJJ, van Heusden GPH. Increased Agrobacterium-mediated transformation of Saccharomyces cerevisiae after deletion of the yeast ADA2 gene. Lett Appl Microbiol 2021; 74:228-237. [PMID: 34816457 PMCID: PMC9299121 DOI: 10.1111/lam.13605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/23/2022]
Abstract
Agrobacterium tumefaciens is the causative agent of crown gall disease and is widely used as a vector to create transgenic plants. Under laboratory conditions, the yeast Saccharomyces cerevisiae and other yeasts and fungi can also be transformed, and Agrobacterium-mediated transformation (AMT) is now considered the method of choice for genetic transformation of many fungi. Unlike plants, in S. cerevisiae, T-DNA is integrated preferentially by homologous recombination and integration by non-homologous recombination is very inefficient. Here we report that upon deletion of ADA2, encoding a component of the ADA and SAGA transcriptional adaptor/histone acetyltransferase complexes, the efficiency of AMT significantly increased regardless of whether integration of T-DNA was mediated by homologous or non-homologous recombination. This correlates with an increase in double-strand DNA breaks, the putative entry sites for T-DNA, in the genome of the ada2Δ deletion mutant, as visualized by the number of Rad52-GFP foci. Our observations may be useful to enhance the transformation of species that are difficult to transform.
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Affiliation(s)
- M R Roushan
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - S Shao
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - I Poledri
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - P J J Hooykaas
- Institute of Biology, Leiden University, Leiden, The Netherlands
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2
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Gong W, Zhou Y, Wang R, Wei X, Zhang L, Dai Y, Zhu Z. Analysis of T-DNA integration events in transgenic rice. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153527. [PMID: 34563791 DOI: 10.1016/j.jplph.2021.153527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Agrobacterium-mediated plant transformation has been widely used for introducing transgene(s) into a plant genome and plant breeding. However, our understanding of T-DNA integration into rice genome remains limited relative to that in the model dicot Arabidopsis. To better elucidate the T-DNA integration into the rice genome, we investigated extensively the T-DNA ends and their flanking rice genomic sequences from two transgenic rice plants carrying Cowpea Trypsin Inhibitor (CpTI)-derived gene Signal-CpTI-KDEL (SCK) and Bacillus thuringiensis (BT) gene, respectively, by TAIL-PCR method. Analysis of the junction sequences between the T-DNA ends and rice genome DNA indicated that there were three joining patterns of microhomology, filler DNA sequences, and exact joining, and both the T-DNA ends tend to adopt identical manner to join the rice genome. After T-DNA integration, there were several variations of rice genomic sequences, including small deletions at the integration sites, superfluous DNA inserted between T-DNA and genome, and translocation of genomic DNA in the flanking regions. The translocation block could be from a noncontiguous region in the same chromosome or different chromosomes at the integration sites, and the originating position of the translocated block resulted in comparable deletion based on a cut/paste mechanism rather than a replication mechanism. Our study may lead to a better understand of T-DNA integration mechanism and facilitate functional genomic studies and further crop improvement.
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Affiliation(s)
- Wankui Gong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Rui Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Chen X, Dong Y, Huang Y, Fan J, Yang M, Zhang J. Whole-genome resequencing using next-generation and Nanopore sequencing for molecular characterization of T-DNA integration in transgenic poplar 741. BMC Genomics 2021; 22:329. [PMID: 33957867 PMCID: PMC8101135 DOI: 10.1186/s12864-021-07625-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular characterization information of T-DNA integration is not only required by public risk assessors and regulators, but is also closely related to the expression of exogenous and endogenous genes. At present, with the development of sequencing technology, whole-genome resequencing has become an attractive approach to identify unknown genetically modified events and characterise T-DNA integration events. RESULTS In this study, we performed genome resequencing of Pb29, a transgenic high-resistance poplar 741 line that has been commercialized, using next-generation and Nanopore sequencing. The results revealed that there are two T-DNA insertion sites, located at 9,283,905-9,283,937 bp on chromosome 3 (Chr03) and 10,868,777-10,868,803 bp on Chr10. The accuracy of the T-DNA insertion locations and directions was verified using polymerase chain reaction amplification. Through sequence alignment, different degrees of base deletions were detected on the T-DNA left and right border sequences, and in the flanking sequences of the insertion sites. An unknown fragment was inserted between the Chr03 insertion site and the right flanking sequence, but the Pb29 genome did not undergo chromosomal rearrangement. It is worth noting that we did not detect the API gene in the Pb29 genome, indicating that Pb29 is a transgenic line containing only the BtCry1AC gene. On Chr03, the insertion of T-DNA disrupted a gene encoding TAF12 protein, but the transcriptional abundance of this gene did not change significantly in the leaves of Pb29. Additionally, except for the gene located closest to the T-DNA integration site, the expression levels of four other neighboring genes did not change significantly in the leaves of Pb29. CONCLUSIONS This study provides molecular characterization information of T-DNA integration in transgenic poplar 741 line Pb29, which contribute to safety supervision and further extensive commercial planting of transgenic poplar 741.
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Affiliation(s)
- Xinghao Chen
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China
| | - Yali Huang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China
| | - Jianmin Fan
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China. .,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China.
| | - Jun Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China. .,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China.
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4
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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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5
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Dehghani J, Movafeghi A, Barzegari A, Barar J. Efficient and stable transformation of Dunaliella pseudosalina by 3 strains of Agrobacterium tumefaciens. ACTA ACUST UNITED AC 2017; 7:247-254. [PMID: 29435432 PMCID: PMC5801536 DOI: 10.15171/bi.2017.29] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022]
Abstract
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Introduction:
Several platforms including mammalian, plant and insect cells as well as bacteria, yeasts, and microalgae are available for the production of recombinant proteins. Low efficiency of delivery systems, extracellular and intracellular degradation of foreign genes during transformation, difficulties in targeting and importing into the nucleus, and finally problems in integration into nuclear genome are the most bottlenecks of classical plasmids for producing recombinant proteins. Owing to high growth rate, no common pathogen with humans, being utilized as humans’ food, and capability to perform N-glycosylation, microalgae are proposed as an ideal system for such biotechnological approaches. Here, Agrobacterium tumefaciens is introduced as an alternative tool for transformation of the microalga Dunaliella pseudosalina.
Methods: The transformation of gfp gene into the D. pseudosalina was evaluated by three strains including EHA101, GV3301 and GV3850 of A. tumefaciens. The integrating and expression of gfp gene were determined by PCR, RT-PCR, Q-PCR and SDS-PAGE analyses.
Results: The T-DNA of pCAMBIA1304 plasmid was successfully integrated into the genome of the microalgal cells. Although all of the strains were able to transform the algal cells, GV3301 possessed higher potential to transform the microalgal cells in comparison to EHA101 and GV3850 strains. Moreover, the stability of gfp gene was successfully established during a course of two months period in the microalgal genome.
Conclusion : Agrobacterium is introduced as a competent system for stable transformation of Dunaliella strains in order to produce eukaryotic recombinant proteins.
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Affiliation(s)
- Jaber Dehghani
- Department of Plant Biology, Faculty of Natural Science, University of Tabriz, 29th Bahman Blvd, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran
| | - Ali Movafeghi
- Department of Plant Biology, Faculty of Natural Science, University of Tabriz, 29th Bahman Blvd, Tabriz, Iran
| | - Abolfazl Barzegari
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran.,School of Advanced Biomedical Sciences, Tabriz University of Medical Science, Daneshgah street, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran
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6
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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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CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing. GENOMICS DATA 2015; 6:175-81. [PMID: 26697366 PMCID: PMC4664744 DOI: 10.1016/j.gdata.2015.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/02/2015] [Indexed: 11/22/2022]
Abstract
Transgenic crops have become a staple in modern agriculture, and are typically characterized using a variety of molecular techniques involving proteomics and metabolomics. Characterization of the transgene insertion site is of great interest, as disruptions, deletions, and genomic location can affect product selection and fitness, and identification of these regions and their integrity is required for regulatory agencies. Here, we present CONTRAILS (Characterization of Transgene Insertion Locations with Sequencing), a straightforward, rapid and reproducible method for the identification of transgene insertion sites in highly complex and repetitive genomes using low coverage paired-end Illumina sequencing and traditional PCR. This pipeline requires little to no troubleshooting and is not restricted to any genome type, allowing use for many molecular applications. Using whole genome sequencing of in-house transgenic Glycine max, a legume with a highly repetitive and complex genome, we used CONTRAILS to successfully identify the location of a single T-DNA insertion to single base resolution. We developed a pipeline for transgene identification using paired-end sequencing. This method requires little troubleshooting and is applicable to any genome. Identification of insertion sites is required for deregulation of modified food crops. This assists in identifying potential genomic disruptions in transgenic events.
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8
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Wang Y, Zeng H, Zhou X, Huang F, Peng W, Liu L, Xiong W, Shi X, Luo M. Transformation of rice with large maize genomic DNA fragments containing high content repetitive sequences. PLANT CELL REPORTS 2015; 34:1049-1061. [PMID: 25700981 DOI: 10.1007/s00299-015-1764-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/28/2015] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Large and complex maize BIBAC inserts, even with a length of about 164 kb and repeat sequences of 88.1%, were transferred into rice. The BIBAC vector has been established to clone large DNA fragments and directly transfer them into plants. Previously, we have constructed a maize B73 BIBAC library and demonstrated that the BIBAC clones were stable in Agrobacterium. In this study, we demonstrated that the maize BIBAC clones could be used for rice genetic transformation through Agrobacterium-mediated method, although the average transformation efficiency for the BIBAC clones (0.86%) is much lower than that for generally used binary vectors containing small DNA fragments (15.24%). The 164-kb B73 genomic DNA insert of the BIBAC clone B2-6 containing five maize gene models and 88.1% of repetitive sequences was transferred into rice. In 18.75% (3/16) of the T1, 13.79% (4/29) of the T2, and 5.26% (1/19) of the T3 generation transgenic rice plants positive for the GUS and HYG marker genes, all the five maize genes can be detected. To our knowledge, this is the largest and highest content of repeat sequence-containing DNA fragment that was successfully transferred into plants. Gene expression analysis (RT-PCR) showed that the expression of three out of five genes could be detected in the leaves of the transgenic rice plants. Our study showed a potential to massively use maize genome resource for rice breeding by mass transformation of rice with large maize genomic DNA fragment BIBAC clones.
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Affiliation(s)
- Yafei Wang
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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9
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McAllister CH, Good AG. Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana. PLoS One 2015; 10:e0121830. [PMID: 25830496 PMCID: PMC4382294 DOI: 10.1371/journal.pone.0121830] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/04/2015] [Indexed: 01/08/2023] Open
Abstract
Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.
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Affiliation(s)
- Chandra H. McAllister
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- * E-mail:
| | - Allen G. Good
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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10
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Dafny-Yelin M, Levy A, Dafny R, Tzfira T. Blocking single-stranded transferred DNA conversion to double-stranded intermediates by overexpression of yeast DNA REPLICATION FACTOR A. PLANT PHYSIOLOGY 2015; 167:153-63. [PMID: 25424309 PMCID: PMC4281008 DOI: 10.1104/pp.114.250639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/23/2014] [Indexed: 05/09/2023]
Abstract
Agrobacterium tumefaciens delivers its single-stranded transferred DNA (T-strand) into the host cell nucleus, where it can be converted into double-stranded molecules. Various studies have revealed that double-stranded transfer DNA (T-DNA) intermediates can serve as substrates by as yet uncharacterized integration machinery. Nevertheless, the possibility that T-strands are themselves substrates for integration cannot be ruled out. We attempted to block the conversion of T-strands into double-stranded intermediates prior to integration in order to further investigate the route taken by T-DNA molecules on their way to integration. Transgenic tobacco (Nicotiana benthamiana) plants that overexpress three yeast (Saccharomyces cerevisiae) protein subunits of DNA REPLICATION FACTOR A (RFA) were produced. In yeast, these subunits (RFA1-RFA3) function as a complex that can bind single-stranded DNA molecules, promoting the repair of genomic double strand breaks. Overexpression of the RFA complex in tobacco resulted in decreased T-DNA expression, as determined by infection with A. tumefaciens cells carrying the β-glucuronidase intron reporter gene. Gene expression was not blocked when the reporter gene was delivered by microbombardment. Enhanced green fluorescent protein-assisted localization studies indicated that the three-protein complex was predominantly nuclear, thus indicating its function within the plant cell nucleus, possibly by binding naked T-strands and blocking their conversion into double-stranded intermediates. This notion was further supported by the inhibitory effect of RFA expression on the cell-to-cell movement of Bean dwarf mosaic virus, a single-stranded DNA virus. The observation that RFA complex plants dramatically inhibited the transient expression level of T-DNA and only reduced T-DNA integration by 50% suggests that double-stranded T-DNA intermediates, as well as single-stranded T-DNA, play significant roles in the integration process.
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Affiliation(s)
- Mery Dafny-Yelin
- Golan Research Institute, University of Haifa, Qatzrin 12900, Israel (M.D.-Y., R.D.);Noga AgroTech Desert Agriculture, Kmehin 85511, Israel (A.L.);Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (R.D., T.T.); andDepartment of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (T.T.)
| | - Avner Levy
- Golan Research Institute, University of Haifa, Qatzrin 12900, Israel (M.D.-Y., R.D.);Noga AgroTech Desert Agriculture, Kmehin 85511, Israel (A.L.);Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (R.D., T.T.); andDepartment of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (T.T.)
| | - Raz Dafny
- Golan Research Institute, University of Haifa, Qatzrin 12900, Israel (M.D.-Y., R.D.);Noga AgroTech Desert Agriculture, Kmehin 85511, Israel (A.L.);Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (R.D., T.T.); andDepartment of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (T.T.)
| | - Tzvi Tzfira
- Golan Research Institute, University of Haifa, Qatzrin 12900, Israel (M.D.-Y., R.D.);Noga AgroTech Desert Agriculture, Kmehin 85511, Israel (A.L.);Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (R.D., T.T.); andDepartment of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (T.T.)
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11
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Wolterink-van Loo S, Ayala AAE, Hooykaas PJJ, van Heusden GPH. Interaction of the Agrobacterium tumefaciens virulence protein VirD2 with histones. MICROBIOLOGY-SGM 2014; 161:401-410. [PMID: 25505187 DOI: 10.1099/mic.0.083410-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Agrobacterium tumefaciens is a Gram-negative soil bacterium that genetically transforms plants and, under laboratory conditions, also transforms non-plant organisms, such as fungi and yeasts. During the transformation process a piece of ssDNA (T-strand) is transferred into the host cells via a type IV secretion system. The VirD2 relaxase protein, which is covalently attached at the 5' end of the T-strand through Tyr29, mediates nuclear entry as it contains a nuclear localization sequence. How the T-strand reaches the chromatin and becomes integrated in the chromosomal DNA is still far from clear. Here, we investigated whether VirD2 binds to histone proteins in the yeast Saccharomyces cerevisiae. Using immobilized GFP-VirD2 and in vitro synthesized His6-tagged S. cerevisiae proteins, interactions between VirD2 and the histones H2A, H2B, H3 and H4 were revealed. In vivo, these interactions were confirmed by bimolecular fluorescence complementation experiments. After co-cultivation of Agrobacterium strains expressing VirD2 tagged with a fragment of the yellow fluorescent protein analogue Venus with yeast strains expressing histone H2A or H2B tagged with the complementary part of Venus, fluorescence was detected in dot-shaped structures in the recipient yeast cells. The results indicated that VirD2 was transferred from Agrobacterium to yeast cells and that it interacted with histones in the host cell, and thus may help direct the T-DNA (transferred DNA) to the chromatin as a prelude to integration into the host chromosomal DNA.
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Affiliation(s)
- Suzanne Wolterink-van Loo
- Section Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Abril A Escamilla Ayala
- Section Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Paul J J Hooykaas
- Section Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - G Paul H van Heusden
- Section Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, The Netherlands
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Abstract
The study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.
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Affiliation(s)
- Craig S Pikaard
- Department of Biology, Department of Molecular and Cellular Biochemistry, and Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405
| | - Ortrun Mittelsten Scheid
- Gregor Mendel-Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
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13
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Abstract
The study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.
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Affiliation(s)
- Craig S Pikaard
- Department of Biology, Department of Molecular and Cellular Biochemistry, and Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405
| | - Ortrun Mittelsten Scheid
- Gregor Mendel-Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
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14
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Agrobacterium-mediated plant transformation: Factors, applications and recent advances. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2013.10.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Wang Y, Peng W, Zhou X, Huang F, Shao L, Luo M. The putative Agrobacterium transcriptional activator-like virulence protein VirD5 may target T-complex to prevent the degradation of coat proteins in the plant cell nucleus. THE NEW PHYTOLOGIST 2014; 203:1266-1281. [PMID: 24865527 DOI: 10.1111/nph.12866] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
Agrobacterium exports at least five virulence proteins (VirE2, VirE3, VirF, VirD2, VirD5) into host cells and hijacks some host plant factors to facilitate its transformation process. Random DNA binding selection assays (RDSAs), electrophoretic mobility shift assays (EMSAs) and yeast one-hybrid systems were used to identify protein-bound DNA elements. Bimolecular fluorescence complementation, glutathione S-transferase pull-down and yeast two-hybrid assays were used to detect protein interactions. Protoplast transformation, coprecipitation, competitive binding and cell-free degradation assays were used to analyze the relationships among proteins. We found that Agrobacterium VirD5 exhibits transcriptional activation activity in yeast, is located in the plant cell nucleus, and forms homodimers. A specific VirD5-bound DNA element designated D5RE (VirD5 response element) was identified. VirD5 interacted directly with Arabidopsis VirE2 Interacting Protein 1 (AtVIP1). However, the ternary complex of VirD5-AtVIP1-VirE2 could be detected, whereas that of VirD5-AtVIP1-VBF (AtVIP1 Binding F-box protein) could not. We demonstrated that VirD5 competes with VBF for binding to AtVIP1 and stabilizes AtVIP1 and VirE2 in the cell-free degradation system. Our results indicated that VirD5 may act as both a transcriptional activator-like effector to regulate host gene expression and a protector preventing the coat proteins of the T-complex from being quickly degraded by the host's ubiquitin proteasome system (UPS).
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Affiliation(s)
- Yafei Wang
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Peng
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Huang
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingyun Shao
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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16
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Bilichak A, Yao Y, Kovalchuk I. Transient down-regulation of the RNA silencing machinery increases efficiency of Agrobacterium-mediated transformation of Arabidopsis. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:590-600. [PMID: 24472037 DOI: 10.1111/pbi.12165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/15/2013] [Indexed: 06/03/2023]
Abstract
Agrobacterium tumefaciens is a plant pathogen that is widely used in plant transformation. As the process of transgenesis includes the delivery of single-stranded T-DNA molecule, we hypothesized that transformation rate may negatively correlate with the efficiency of the RNA-silencing machinery. Using mutants compromised in either the transcriptional or post-transcriptional gene-silencing pathways, two inhibitors of stable transformation were revealed-AGO2 and NRPD1a. Furthermore, an immunoprecipitation experiment has shown that NRPD1, a subunit of Pol IV, directly interacts with Agrobacterium T-DNA in planta. Using the Tobacco rattle virus (TRV)--based virus-induced gene silencing (VIGS) technique, we demonstrated that the transient down-regulation of the expression of either AGO2 or NRPD1a genes in reproductive organs of Arabidopsis, leads to an increase in transformation rate. We observed a 6.0- and 3.5-fold increase in transformation rate upon transient downregulation of either AGO2 or NRPD1a genes, respectively. This is the first report demonstrating the increase in the plant transformation rate via VIGS-mediated transient down-regulation of the components of epigenetic machinery in reproductive tissue.
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MESH Headings
- Agrobacterium/physiology
- Arabidopsis/genetics
- Arabidopsis/microbiology
- Arabidopsis Proteins/metabolism
- Blotting, Southern
- DNA Breaks, Double-Stranded
- DNA Methylation/genetics
- DNA, Bacterial/genetics
- DNA-Directed RNA Polymerases/metabolism
- Down-Regulation
- Epigenesis, Genetic
- Genes, Plant
- Genetic Loci
- Models, Genetic
- Mutation/genetics
- Plants, Genetically Modified
- Protein Binding
- Protein Subunits/metabolism
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Reverse Genetics
- Transformation, Genetic
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Affiliation(s)
- Andriy Bilichak
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
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17
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Gohlke J, Deeken R. Plant responses to Agrobacterium tumefaciens and crown gall development. FRONTIERS IN PLANT SCIENCE 2014; 5:155. [PMID: 24795740 PMCID: PMC4006022 DOI: 10.3389/fpls.2014.00155] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/02/2014] [Indexed: 05/17/2023]
Abstract
Agrobacterium tumefaciens causes crown gall disease on various plant species by introducing its T-DNA into the genome. Therefore, Agrobacterium has been extensively studied both as a pathogen and an important biotechnological tool. The infection process involves the transfer of T-DNA and virulence proteins into the plant cell. At that time the gene expression patterns of host plants differ depending on the Agrobacterium strain, plant species and cell-type used. Later on, integration of the T-DNA into the plant host genome, expression of the encoded oncogenes, and increase in phytohormone levels induce a fundamental reprogramming of the transformed cells. This results in their proliferation and finally formation of plant tumors. The process of reprogramming is accompanied by altered gene expression, morphology and metabolism. In addition to changes in the transcriptome and metabolome, further genome-wide ("omic") approaches have recently deepened our understanding of the genetic and epigenetic basis of crown gall tumor formation. This review summarizes the current knowledge about plant responses in the course of tumor development. Special emphasis is placed on the connection between epigenetic, transcriptomic, metabolomic, and morphological changes in the developing tumor. These changes not only result in abnormally proliferating host cells with a heterotrophic and transport-dependent metabolism, but also cause differentiation and serve as mechanisms to balance pathogen defense and adapt to abiotic stress conditions, thereby allowing the coexistence of the crown gall and host plant.
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Affiliation(s)
- Jochen Gohlke
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | - Rosalia Deeken
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of WuerzburgWuerzburg, Germany
- *Correspondence: Rosalia Deeken, Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Wuerzburg, Julius-von-Sachs-Platz 2, 97082 Wuerzburg, Germany e-mail:
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18
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Saika H, Nishizawa-Yokoi A, Toki S. The non-homologous end-joining pathway is involved in stable transformation in rice. FRONTIERS IN PLANT SCIENCE 2014; 5:560. [PMID: 25368624 PMCID: PMC4201092 DOI: 10.3389/fpls.2014.00560] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/29/2014] [Indexed: 05/20/2023]
Abstract
Stable transformation with T-DNA needs the coordinated activities of many proteins derived from both host plant cells and Agrobacterium. In dicot plants, including Arabidopsis, it has been suggested that non-homologous end-joining (NHEJ)-one of the main DNA double-strand break repair pathways-is involved in the T-DNA integration step that is crucial to stable transformation. However, how this pathway is involved remains unclear as results with NHEJ mutants in Arabidopsis have given inconsistent results. Recently, a system for visualization of stable expression of genes located on T-DNA has been established in rice callus. Stable expression was shown to be reduced significantly in NHEJ knock-down rice calli, suggesting strongly that NHEJ is involved in Agrobacterium-mediated stable transformation in rice. Since rice transformation is now efficient and reproducible, rice is a good model plant in which to elucidate the molecular mechanisms of T-DNA integration.
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Affiliation(s)
- Hiroaki Saika
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
- *Correspondence: Hiroaki Saika, Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan e-mail:
| | - Ayako Nishizawa-Yokoi
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
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19
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Bilichak A, Kovalchuk I. Manipulation of epigenetic factors and the DNA repair machinery for improving the frequency of plant transformation. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2013.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chumakov MI. Protein apparatus for horizontal transfer of agrobacterial T-DNA to eukaryotic cells. BIOCHEMISTRY (MOSCOW) 2013; 78:1321-32. [DOI: 10.1134/s000629791312002x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Elmer JJ, Christensen MD, Rege K. Applying horizontal gene transfer phenomena to enhance non-viral gene therapy. J Control Release 2013; 172:246-257. [PMID: 23994344 PMCID: PMC4258102 DOI: 10.1016/j.jconrel.2013.08.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/17/2013] [Accepted: 08/20/2013] [Indexed: 12/25/2022]
Abstract
Horizontal gene transfer (HGT) is widespread amongst prokaryotes, but eukaryotes tend to be far less promiscuous with their genetic information. However, several examples of HGT from pathogens into eukaryotic cells have been discovered and mimicked to improve non-viral gene delivery techniques. For example, several viral proteins and DNA sequences have been used to significantly increase cytoplasmic and nuclear gene delivery. Plant genetic engineering is routinely performed with the pathogenic bacterium Agrobacterium tumefaciens and similar pathogens (e.g. Bartonella henselae) may also be able to transform human cells. Intracellular parasites like Trypanosoma cruzi may also provide new insights into overcoming cellular barriers to gene delivery. Finally, intercellular nucleic acid transfer between host cells will also be briefly discussed. This article will review the unique characteristics of several different viruses and microbes and discuss how their traits have been successfully applied to improve non-viral gene delivery techniques. Consequently, pathogenic traits that originally caused diseases may eventually be used to treat many genetic diseases.
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Affiliation(s)
- Jacob J Elmer
- Department of Chemical Engineering, Villanova University, Villanova 19085, USA.
| | | | - Kaushal Rege
- Chemical Engineering, Arizona State University, Tempe 85287-6106, USA.
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22
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Heisel TJ, Li CY, Grey KM, Gibson SI. Mutations in HISTONE ACETYLTRANSFERASE1 affect sugar response and gene expression in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2013; 4:245. [PMID: 23882272 PMCID: PMC3713338 DOI: 10.3389/fpls.2013.00245] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/19/2013] [Indexed: 05/23/2023]
Abstract
Nutrient response networks are likely to have been among the first response networks to evolve, as the ability to sense and respond to the levels of available nutrients is critical for all organisms. Although several forward genetic screens have been successful in identifying components of plant sugar-response networks, many components remain to be identified. Toward this end, a reverse genetic screen was conducted in Arabidopsis thaliana to identify additional components of sugar-response networks. This screen was based on the rationale that some of the genes involved in sugar-response networks are likely to be themselves sugar regulated at the steady-state mRNA level and to encode proteins with activities commonly associated with response networks. This rationale was validated by the identification of hac1 mutants that are defective in sugar response. HAC1 encodes a histone acetyltransferase. Histone acetyltransferases increase transcription of specific genes by acetylating histones associated with those genes. Mutations in HAC1 also cause reduced fertility, a moderate degree of resistance to paclobutrazol and altered transcript levels of specific genes. Previous research has shown that hac1 mutants exhibit delayed flowering. The sugar-response and fertility defects of hac1 mutants may be partially explained by decreased expression of AtPV42a and AtPV42b, which are putative components of plant SnRK1 complexes. SnRK1 complexes have been shown to function as central regulators of plant nutrient and energy status. Involvement of a histone acetyltransferase in sugar response provides a possible mechanism whereby nutritional status could exert long-term effects on plant development and metabolism.
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Affiliation(s)
| | | | | | - Susan I. Gibson
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of MinnesotaSaint Paul, MN, USA
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23
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Gleba YY, Tusé D, Giritch A. Plant viral vectors for delivery by Agrobacterium. Curr Top Microbiol Immunol 2013; 375:155-92. [PMID: 23949286 DOI: 10.1007/82_2013_352] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Plant viral vectors delivered by Agrobacterium are the basis of several manufacturing processes that are currently in use for producing a wide range of proteins for multiple applications, including vaccine antigens, antibodies, protein nanoparticles such as virus-like particles (VLPs), and other protein and protein-RNA scaffolds. Viral vectors delivered by agrobacterial T-DNA transfer (magnifection) have also become important tools in research. In recent years, essential advances have been made both in the development of second-generation vectors designed using the 'deconstructed virus' approach, as well as in the development of upstream manufacturing processes that are robust and fully scalable. The strategy relies on Agrobacterium as a vector to deliver DNA copies of one or more viral RNA/DNA replicons; the bacteria are delivered into leaves by vacuum infiltration, and the viral machinery takes over from the point of T-DNA transfer to the plant cell nucleus, driving massive RNA and protein production and, if required, cell-to-cell spread of the replicons. Among the most often used viral backbones are those of the RNA viruses Tobacco mosaic virus (TMV), Potato virus X (PVX) and Cowpea mosaic virus (CPMV), and the DNA geminivirus Bean yellow dwarf virus. Prototypes of industrial processes that provide for high yield, rapid scale up and fast manufacturing cycles have been designed, and several GMP-compliant and GMP-certified manufacturing facilities are in place. These efforts have been successful as evidenced by the fact that several antibodies and vaccine antigens produced by magnifection are currently in clinical development.
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Affiliation(s)
- Yuri Y Gleba
- Nomad Bioscience GmbH, Weinbergweg 22, Halle (Saale), Germany,
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24
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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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25
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Nishizawa-Yokoi A, Nonaka S, Saika H, Kwon YI, Osakabe K, Toki S. Suppression of Ku70/80 or Lig4 leads to decreased stable transformation and enhanced homologous recombination in rice. THE NEW PHYTOLOGIST 2012; 196:1048-1059. [PMID: 23050791 PMCID: PMC3532656 DOI: 10.1111/j.1469-8137.2012.04350.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/23/2012] [Indexed: 05/13/2023]
Abstract
Evidence for the involvement of the nonhomologous end joining (NHEJ) pathway in Agrobacterium-mediated transferred DNA (T-DNA) integration into the genome of the model plant Arabidopsis remains inconclusive. Having established a rapid and highly efficient Agrobacterium-mediated transformation system in rice (Oryza sativa) using scutellum-derived calli, we examined here the involvement of the NHEJ pathway in Agrobacterium-mediated stable transformation in rice. Rice calli from OsKu70, OsKu80 and OsLig4 knockdown (KD) plants were infected with Agrobacterium harboring a sensitive emerald luciferase (LUC) reporter construct to evaluate stable expression and a green fluorescent protein (GFP) construct to monitor transient expression of T-DNA. Transient expression was not suppressed, but stable expression was reduced significantly, in KD plants. Furthermore, KD-Ku70 and KD-Lig4 calli exhibited an increase in the frequency of homologous recombination (HR) compared with control calli. In addition, suppression of OsKu70, OsKu80 and OsLig4 induced the expression of HR-related genes on treatment with DNA-damaging agents. Our findings suggest strongly that NHEJ is involved in Agrobacterium-mediated stable transformation in rice, and that there is a competitive and complementary relationship between the NHEJ and HR pathways for DNA double-strand break repair in rice.
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Affiliation(s)
- Ayako Nishizawa-Yokoi
- Plant Genome Engineering Research Unit, National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Satoko Nonaka
- Plant Genome Engineering Research Unit, National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hiroaki Saika
- Plant Genome Engineering Research Unit, National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yong-Ik Kwon
- Plant Genome Engineering Research Unit, National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Kihara Institute for Biological Research, Yokohama City University641-12 Maioka-cho, Yokohama 244-0813, Japan
| | - Keishi Osakabe
- Plant Genome Engineering Research Unit, National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Institute for Environmental Science and Technology, Saitama UniversityShimo-Okubo 255, Sakura-ku, Saitama-shi, 338-8570 Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Kihara Institute for Biological Research, Yokohama City University641-12 Maioka-cho, Yokohama 244-0813, Japan
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Delporte F, Jacquemin JM, Masson P, Watillon B. Insights into the regenerative property of plant cells and their receptivity to transgenesis: wheat as a research case study. PLANT SIGNALING & BEHAVIOR 2012; 7:1608-20. [PMID: 23072995 PMCID: PMC3578902 DOI: 10.4161/psb.22424] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
From a holistic perspective, the discovery of cellular plasticity, a very interesting property of totipotency, underlies many topical issues in biology with important medical applications, while transgenesis is a core research tool in biology. Partially known, some basic mechanisms involved in the regenerative property of cells and in their receptivity to transgenesis are common to plant and animal cells and highlight the principle of the unity of life. Transgenesis provides an important investigative instrument in plant physiology and is regarded as a valuable tool for crop improvement. The economic, social, cultural and scientific importance of cereals has led to a rich stream of research into their genetics, biology and evolution. Sustained efforts to achieve the results obtained in the fields of genetic engineering and applied biotechnology reflect this deep interest. Difficulties encountered in creating genetically modified cereals, especially wheat, highlighted the central notions of tissue culture regeneration and transformation competencies. From the perspective of combining or encountering these competencies in the same cell lineage, this reputedly recalcitrant species provides a stimulating biological system in which to explore the physiological and genetic complexity of both competencies. The former involves two phases, dedifferentiation and redifferentiation. Cells undergo development switches regulated by extrinsic and intrinsic factors. The re-entry into the cell division cycle progressively culminates in the development of organized structures. This is achieved by global chromatin reorganization associated with the reprogramming of the gene expression pattern. The latter is linked with surveillance mechanisms and DNA repair, aimed at maintaining genome integrity before cells move into mitosis, and with those mechanisms aimed at genome expression control and regulation. In order to clarify the biological basis of these two physiological properties and their interconnectedness, we look at both competencies at the core of defense/adaptive mechanisms and survival, between undifferentiated cell proliferation and organization, constituting a transition phase between two different dynamic regimes, a typical feature of critical dynamic systems. Opting for a candidate-gene strategy, several gene families could be proposed as relevant targets for investigating this hypothesis at the molecular level.
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Affiliation(s)
- Fabienne Delporte
- Walloon Agricultural Research Centre (CRAw), Department of Life Sciences, Bioengineering Unit, Gembloux, Belgium.
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Mehrotra S, Goyal V. Agrobacterium-mediated gene transfer in plants and biosafety considerations. Appl Biochem Biotechnol 2012; 168:1953-75. [PMID: 23090683 DOI: 10.1007/s12010-012-9910-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/03/2012] [Indexed: 12/21/2022]
Abstract
Agrobacterium, the natures' genetic engineer, has been used as a vector to create transgenic plants. Agrobacterium-mediated gene transfer in plants is a highly efficient transformation process which is governed by various factors including genotype of the host plant, explant, vector, plasmid, bacterial strain, composition of culture medium, tissue damage, and temperature of co-cultivation. Agrobacterium has been successfully used to transform various economically and horticulturally important monocot and dicot species by standard tissue culture and in planta transformation techniques like floral or seedling infilteration, apical meristem transformation, and the pistil drip methods. Monocots have been comparatively difficult to transform by Agrobacterium. However, successful transformations have been reported in the last few years based on the adjustment of the parameters that govern the responses of monocots to Agrobacterium. A novel Agrobacterium transferred DNA-derived nanocomplex method has been developed which will be highly valuable for plant biology and biotechnology. Agrobacterium-mediated genetic transformation is known to be the preferred method of creating transgenic plants from a commercial and biosafety perspective. Agrobacterium-mediated gene transfer predominantly results in the integration of foreign genes at a single locus in the host plant, without associated vector backbone and is also known to produce marker free plants, which are the prerequisites for commercialization of transgenic crops. Research in Agrobacterium-mediated transformation can provide new and novel insights into the understanding of the regulatory process controlling molecular, cellular, biochemical, physiological, and developmental processes occurring during Agrobacterium-mediated transformation and also into a wide range of aspects on biological safety of transgenic crops to improve crop production to meet the demands of ever-growing world's population.
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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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Abstract
The nucleus, at the heart of the eukaryotic cell, hosts and protects the genetic material, governs gene expression and regulates the whole cell physiology, including cell division. A growing number of studies indicate that various animal and plant pathogenic bacteria can deliver factors to this central organelle to subvert host defences by directly interfering with transcription, chromatin-remodelling, RNA splicing or DNA replication and repair. Such bacterial molecules entering the nucleus, which we propose to term 'nucleomodulins', use diverse strategies to hijack nuclear processes by targeting host DNA or an array of nuclear proteins. In some cases, bacteria can even enter the nucleus. These bacterial 'nuclear attacks' might have permanent genetic or long-term epigenetic effects on the host. Studying nucleomodulins and endonuclear bacteria can thus generate new insights into long-term impacts of infectious diseases and create novel tools for biotechnological applications and for deciphering the regulation of nuclear dynamics.
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Affiliation(s)
- Hélène Bierne
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015, France.
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