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Gong J, Yang J, Lai Y, Pan T, She W. A High-Quality Assembly and Comparative Analysis of the Mitogenome of Actinidia macrosperma. Genes (Basel) 2024; 15:514. [PMID: 38674448 PMCID: PMC11049864 DOI: 10.3390/genes15040514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The mitochondrial genome (mitogenome) of Actinidia macrosperma, a traditional medicinal plant within the Actinidia genus, remains relatively understudied. This study aimed to sequence the mitogenome of A. macrosperma, determining its assembly, informational content, and developmental expression. The results revealed that the mitogenome of A. macrosperma is circular, spanning 752,501 bp with a GC content of 46.16%. It comprises 63 unique genes, including 39 protein-coding genes (PCGs), 23 tRNA genes, and three rRNA genes. Moreover, the mitogenome was found to contain 63 SSRs, predominantly mono-nucleotides, as well as 25 tandem repeats and 650 pairs of dispersed repeats, each with lengths equal to or greater than 60, mainly comprising forward repeats and palindromic repeats. Moreover, 53 homologous fragments were identified between the mitogenome and chloroplast genome (cp-genome), with the longest segment measuring 4296 bp. This study represents the initial report on the mitogenome of the A. macrosperma, providing crucial genetic materials for phylogenetic research within the Actinidia genus and promoting the exploitation of species genetic resources.
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Affiliation(s)
- Jiangmei Gong
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jun Yang
- College of Food and Bioengineering, Bengbu University, Bengbu 233030, China;
| | - Yan Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tengfei Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenqin She
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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2
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Merker L, Feller L, Dorn A, Puchta H. Deficiency of both classical and alternative end-joining pathways leads to a synergistic defect in double-strand break repair but not to an increase in homology-dependent gene targeting in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:242-254. [PMID: 38179887 DOI: 10.1111/tpj.16604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/13/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
In eukaryotes, double-strand breaks (DSBs) are either repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ). In somatic plant cells, HR is very inefficient. Therefore, the vast majority of DSBs are repaired by two different pathways of NHEJ. The classical (cNHEJ) pathway depends on the heterodimer KU70/KU80, while polymerase theta (POLQ) is central to the alternative (aNHEJ) pathway. Surprisingly, Arabidopsis plants are viable, even when both pathways are impaired. However, they exhibit severe growth retardation and reduced fertility. Analysis of mitotic anaphases indicates that the double mutant is characterized by a dramatic increase in chromosome fragmentation due to defective DSB repair. In contrast to the single mutants, the double mutant was found to be highly sensitive to the DSB-inducing genotoxin bleomycin. Thus, both pathways can complement for each other efficiently in DSB repair. We speculated that in the absence of both NHEJ pathways, HR might be enhanced. This would be especially attractive for gene targeting (GT) in which predefined changes are introduced using a homologous template. Unexpectedly, the polq single mutant as well as the double mutant showed significantly lower GT frequencies in comparison to wildtype plants. Accordingly, we were able to show that elimination of both NHEJ pathways does not pose an attractive approach for Agrobacterium-mediated GT. However, our results clearly indicate that a loss of cNHEJ leads to an increase in GT frequency, which is especially drastic and attractive for practical applications, in which the in planta GT strategy is used.
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Affiliation(s)
- Laura Merker
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Laura Feller
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Annika Dorn
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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3
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Samach A, Mafessoni F, Gross O, Melamed-Bessudo C, Filler-Hayut S, Dahan-Meir T, Amsellem Z, Pawlowski WP, Levy AA. CRISPR/Cas9-induced DNA breaks trigger crossover, chromosomal loss, and chromothripsis-like rearrangements. THE PLANT CELL 2023; 35:3957-3972. [PMID: 37497643 PMCID: PMC10615209 DOI: 10.1093/plcell/koad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
DNA double-stranded breaks (DSBs) generated by the Cas9 nuclease are commonly repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR). However, little is known about unrepaired DSBs and the type of damage they trigger in plants. We designed an assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay, we detected a tomato (Solanum lycopersicum) flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole-genome sequencing and molecular and cytological analyses supports a model in which a breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a tool for precise breeding via targeted crossover detection. It also uncovers CRISPR-mediated chromothripsis-like events in plants.
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Affiliation(s)
- Aviva Samach
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Fabrizio Mafessoni
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Or Gross
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Cathy Melamed-Bessudo
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Shdema Filler-Hayut
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Tal Dahan-Meir
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Ziva Amsellem
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | | | - Avraham A Levy
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
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4
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Zhang X, Shan Y, Li J, Qin Q, Yu J, Deng H. Assembly of the Complete Mitochondrial Genome of Pereskia aculeata Revealed That Two Pairs of Repetitive Elements Mediated the Recombination of the Genome. Int J Mol Sci 2023; 24:ijms24098366. [PMID: 37176072 PMCID: PMC10179450 DOI: 10.3390/ijms24098366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Pereskia aculeata is a potential new crop species that has both food and medicinal (antinociceptive activity) properties. However, comprehensive genomic research on P. aculeata is still lacking, particularly concerning its organelle genome. In this study, P. aculeata was studied to sequence the mitochondrial genome (mitogenome) and to ascertain the assembly, informational content, and developmental expression of the mitogenome. The findings revealed that the mitogenome of P. aculeata is circular and measures 515,187 bp in length with a GC content of 44.05%. It contains 52 unique genes, including 33 protein-coding genes, 19 tRNA genes, and three rRNA genes. Additionally, the mitogenome analysis identified 165 SSRs, primarily consisting of tetra-nucleotides, and 421 pairs of dispersed repeats with lengths greater than or equal to 30, which were mainly forward repeats. Based on long reads and PCR experiments, we confirmed that two pairs of long-fragment repetitive elements were highly involved with the mitogenome recombination process. Furthermore, there were 38 homologous fragments detected between the mitogenome and chloroplast genome, and the longest fragment was 3962 bp. This is the first report on the mitogenome in the family Cactaceae. The decoding of the mitogenome of P. aculeata will provide important genetic materials for phylogenetic studies of Cactaceae and promote the utilization of species germplasm resources.
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Affiliation(s)
- Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Qiulin Qin
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing 400715, China
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5
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CRISPR/Cas9-Mediated Targeted DNA Integration: Rearrangements at the Junction of Plant and Plasmid DNA. Int J Mol Sci 2022; 23:ijms23158636. [PMID: 35955778 PMCID: PMC9369344 DOI: 10.3390/ijms23158636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022] Open
Abstract
Targeted DNA integration into known locations in the genome has potential advantages over the random insertional events typically achieved using conventional means of genetic modification. We studied the presence and extent of DNA rearrangements at the junction of plant and transgenic DNA in five lines of Arabidopsis thaliana suspension cells carrying a site-specific integration of target genes. Two types of templates were used to obtain knock-ins, differing in the presence or absence of flanking DNA homologous to the target site in the genome. For the targeted insertion, we selected the region of the histone H3.3 gene with a very high constitutive level of expression. Our studies showed that all five obtained knock-in cell lines have rearrangements at the borders of the integrated sequence. Significant rearrangements, about 100 or more bp from the side of the right flank, were found in all five plant lines. Reorganizations from the left flank at more than 17 bp were found in three out of five lines. The fact that rearrangements were detected for both variants of the knock-in template (with and without flanks) indicates that the presence of flanks does not affect the occurrence of mutations.
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6
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Kumar S, Liu ZB, Sanyour-Doyel N, Lenderts B, Worden A, Anand A, Cho HJ, Bolar J, Harris C, Huang L, Xing A, Richardson A. Efficient gene targeting in soybean using Ochrobactrum haywardense-mediated delivery of a marker-free donor template. PLANT PHYSIOLOGY 2022; 189:585-594. [PMID: 35191500 PMCID: PMC9157123 DOI: 10.1093/plphys/kiac075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/24/2022] [Indexed: 05/24/2023]
Abstract
Gene targeting (GT) for precise gene insertion or swap into pre-defined genomic location has been a bottleneck for expedited soybean precision breeding. We report a robust selectable marker-free GT system in soybean, one of the most economically important crops. An efficient Oh H1-8 (Ochrobactrum haywardense H1-8)-mediated embryonic axis transformation method was used for the delivery of CRISPR-Cas9 components and donor template to regenerate T0 plants 6-8 weeks after transformation. This approach generated up to 3.4% targeted insertion of the donor sequence into the target locus in T0 plants, with ∼ 90% mutation rate observed at the genomic target site. The GT was demonstrated in two genomic sites using two different donor DNA templates without the need for a selectable marker within the template. High-resolution Southern-by-Sequencing analysis identified T1 plants with precise targeted insertion and without unintended plasmid DNA. Unlike previous low-frequency GT reports in soybean that involved particle bombardment-mediated delivery and extensive selection, the method described here is fast, efficient, reproducible, does not require a selectable marker within the donor DNA, and generates nonchimeric plants with heritable GT.
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Affiliation(s)
| | | | | | | | | | - Ajith Anand
- Corteva Agriscience, Johnston, Iowa 50131, USA
| | | | - Joy Bolar
- Corteva Agriscience, Johnston, Iowa 50131, USA
| | | | | | - Aiqiu Xing
- Corteva Agriscience, Johnston, Iowa 50131, USA
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7
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Kausch AP, Wang K, Kaeppler HF, Gordon-Kamm W. Maize transformation: history, progress, and perspectives. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:38. [PMID: 37309443 PMCID: PMC10236110 DOI: 10.1007/s11032-021-01225-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/14/2021] [Indexed: 06/14/2023]
Abstract
Maize functional genomics research and genetic improvement strategies have been greatly accelerated and refined through the development and utilization of genetic transformation systems. Maize transformation is a composite technology based on decades' efforts in optimizing multiple factors involving microbiology and physical/biochemical DNA delivery, as well as cellular and molecular biology. This review provides a historical reflection on the development of maize transformation technology including the early failures and successful milestones. It also provides a current perspective on the understanding of tissue culture responses and their impact on plant regeneration, the pros and cons of different DNA delivery methods, the identification of a palette of selectable/screenable markers, and most recently the development of growth-stimulating or morphogenic genes to improve efficiencies and extend the range of transformable genotypes. Steady research progress in these interdependent components has been punctuated by benchmark reports celebrating the progress in maize transformation, which invariably relied on a large volume of supporting research that contributed to each step and to the current state of the art. The recent explosive use of CRISPR/Cas9-mediated genome editing has heightened the demand for higher transformation efficiencies, especially for important inbreds, to support increasingly sophisticated and complicated genomic modifications, in a manner that is widely accessible. These trends place an urgent demand on taking maize transformation to the next level, presaging a new generation of improvements on the horizon. Once realized, we anticipate a near-future where readily accessible, genotype-independent maize transformation, together with advanced genomics, genome editing, and accelerated breeding, will contribute to world agriculture and global food security.
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Affiliation(s)
- Albert P. Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, RI 02892 USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
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8
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Barone P, Wu E, Lenderts B, Anand A, Gordon-Kamm W, Svitashev S, Kumar S. Efficient Gene Targeting in Maize Using Inducible CRISPR-Cas9 and Marker-free Donor Template. MOLECULAR PLANT 2020; 13:1219-1227. [PMID: 32574856 DOI: 10.1016/j.molp.2020.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 05/26/2023]
Abstract
CRISPR-Cas9 is a powerful tool for generating targeted mutations and genomic deletions. However, precise gene insertion or sequence replacement remains a major hurdle before application of CRISPR-Cas9 technology is fully realized in plant breeding. Here, we report high-frequency, selectable marker-free intra-genomic gene targeting (GT) in maize. Heat shock-inducible Cas9 was used for generating targeted double-strand breaks and simultaneous mobilization of the donor template from pre-integrated T-DNA. The construct was designed such that release of the donor template and subsequent DNA repair activated expression of the selectable marker gene within the donor locus. This approach generated up to 4.7% targeted insertion of the donor sequence into the target locus in T0 plants, with up to 86% detected donor template release and 99% mutation rate being observed at the donor loci and the genomic target site, respectively. Unlike previous in planta or intra-genomic homologous recombination reports in which the original chimeric GT plants required extensive progeny screening in the next generation to identify non-chimeric GT individuals, our method provides non-chimeric heritable GT in one generation.
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Affiliation(s)
| | - Emily Wu
- Corteva Agriscience™, Johnston, IA 50131, USA
| | | | - Ajith Anand
- Corteva Agriscience™, Johnston, IA 50131, USA
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9
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Liu HJ, Jian L, Xu J, Zhang Q, Zhang M, Jin M, Peng Y, Yan J, Han B, Liu J, Gao F, Liu X, Huang L, Wei W, Ding Y, Yang X, Li Z, Zhang M, Sun J, Bai M, Song W, Chen H, Sun X, Li W, Lu Y, Liu Y, Zhao J, Qian Y, Jackson D, Fernie AR, Yan J. High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize. THE PLANT CELL 2020; 32:1397-1413. [PMID: 32102844 PMCID: PMC7203946 DOI: 10.1105/tpc.19.00934] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/06/2020] [Accepted: 02/21/2020] [Indexed: 05/19/2023]
Abstract
Maize (Zea mays) is one of the most important crops in the world. However, few agronomically important maize genes have been cloned and used for trait improvement, due to its complex genome and genetic architecture. Here, we integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition. After low-cost barcode-based deep sequencing, 412 edited sequences covering 118 genes were precisely identified from individuals showing clear phenotypic changes. The profiles of the associated gene-editing events were similar to those identified in human cell lines and consequently are predictable using an existing algorithm originally designed for human studies. We observed unexpected but frequent homology-directed repair through endogenous templates that was likely caused by spatial contact between distinct chromosomes. Based on the characterization and interpretation of gene function from several examples, we demonstrate that the integration of forward and reverse genetics via a targeted mutagenesis library promises rapid validation of important agronomic genes for crops with complex genomes. Beyond specific findings, this study also guides further optimization of high-throughput CRISPR experiments in plants.
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Affiliation(s)
- Hai-Jun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jieting Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Maolin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiali Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Baozhu Han
- WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Gao
- Xishuangbanna Institute of Agricultural Science, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xiangguo Liu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Lei Huang
- WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Wenjie Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunxiu Ding
- Xishuangbanna Institute of Agricultural Science, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xiaofeng Yang
- WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Zhenxian Li
- Xishuangbanna Institute of Agricultural Science, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Mingliang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiamin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Minji Bai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhao Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanmo Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi'ang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuming Lu
- Biogle Genome Editing Center, Changzhou 213125, China
| | - Ya Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100097, China
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100097, China
| | - Yangwen Qian
- WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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10
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Taagen E, Bogdanove AJ, Sorrells ME. Counting on Crossovers: Controlled Recombination for Plant Breeding. TRENDS IN PLANT SCIENCE 2020; 25:455-465. [PMID: 31959421 DOI: 10.1016/j.tplants.2019.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/03/2019] [Accepted: 12/11/2019] [Indexed: 05/02/2023]
Abstract
Crossovers (COs), that drive genetic exchange between homologous chromosomes, are strongly biased toward subtelomeric regions in plant species. Manipulating the rate and positions of COs to increase the genetic variation accessible to breeders is a longstanding goal. Use of genome editing reagents that induce double-stranded breaks (DSBs) or modify the epigenome at desired sites of recombination, and manipulation of CO factors, are increasingly applicable approaches for achieving this goal. These strategies for 'controlled recombination' have potential to reduce the time and expense associated with traditional breeding, reveal currently inaccessible genetic diversity, and increase control over the inheritance of preferred haplotypes. Considerable challenges to address include translating knowledge from models to crop species and determining the best stages of the breeding cycle at which to control recombination.
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Affiliation(s)
- Ella Taagen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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11
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Amundson KR, Ordoñez B, Santayana M, Tan EH, Henry IM, Mihovilovich E, Bonierbale M, Comai L. Genomic Outcomes of Haploid Induction Crosses in Potato ( Solanum tuberosum L.). Genetics 2020; 214:369-380. [PMID: 31871130 PMCID: PMC7017018 DOI: 10.1534/genetics.119.302843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/09/2019] [Indexed: 01/12/2023] Open
Abstract
The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.
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Affiliation(s)
- Kirk R Amundson
- Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Benny Ordoñez
- Plant Biology and Genome Center, University of California, Davis, California 95616
- International Potato Center (CIP), Lima 12, Peru
| | | | - Ek Han Tan
- Plant Biology and Genome Center, University of California, Davis, California 95616
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Isabelle M Henry
- Plant Biology and Genome Center, University of California, Davis, California 95616
| | | | | | - Luca Comai
- Plant Biology and Genome Center, University of California, Davis, California 95616
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12
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Grohmann L, Keilwagen J, Duensing N, Dagand E, Hartung F, Wilhelm R, Bendiek J, Sprink T. Detection and Identification of Genome Editing in Plants: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2019; 10:236. [PMID: 30930911 PMCID: PMC6423494 DOI: 10.3389/fpls.2019.00236] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/21/2023]
Abstract
Conventional genetic engineering techniques generate modifications in the genome via stable integration of DNA elements which do not occur naturally in this combination. Therefore, the resulting organisms and (most) products thereof can unambiguously be identified with event-specific PCR-based methods targeting the insertion site. New breeding techniques such as genome editing diversify the toolbox to generate genetic variability in plants. Several of these techniques can introduce single nucleotide changes without integrating foreign DNA and thereby generate organisms with intended phenotypes. Consequently, such organisms and products thereof might be indistinguishable from naturally occurring or conventionally bred counterparts with established analytical tools. The modifications can entirely resemble random mutations regardless of being spontaneous or induced chemically or via irradiation. Therefore, if an identification of these organisms or products thereof is demanded, a new challenge will arise for (official) seed, food, and feed testing laboratories and enforcement institutions. For detailed consideration, we distinguish between the detection of sequence alterations - regardless of their origin - the identification of the process that generated a specific modification and the identification of a genotype, i.e., an organism produced by genome editing carrying a specific genetic alteration in a known background. This article briefly reviews the existing and upcoming detection and identification strategies (including the use of bioinformatics and statistical approaches) in particular for plants developed with genome editing techniques.
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Affiliation(s)
- Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
- *Correspondence: Lutz Grohmann,
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Nina Duensing
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Emilie Dagand
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Frank Hartung
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Joachim Bendiek
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Thorben Sprink
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
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13
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Schmidt C, Pacher M, Puchta H. DNA Break Repair in Plants and Its Application for Genome Engineering. Methods Mol Biol 2019; 1864:237-266. [PMID: 30415341 DOI: 10.1007/978-1-4939-8778-8_17] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome engineering is a biotechnological approach to precisely modify the genetic code of a given organism in order to change the context of an existing sequence or to create new genetic resources, e.g., for obtaining improved traits or performance. Efficient targeted genome alterations are mainly based on the induction of DNA double-strand breaks (DSBs) or adjacent single-strand breaks (SSBs). Naturally, all organisms continuously have to deal with DNA-damaging factors challenging the genetic integrity, and therefore a wide range of DNA repair mechanisms have evolved. A profound understanding of the different repair pathways is a prerequisite to control and enhance targeted gene modifications. DSB repair can take place by nonhomologous end joining (NHEJ) or homology-dependent repair (HDR). As the main outcome of NHEJ-mediated repair is accompanied by small insertions and deletions, it is applicable to specifically knock out genes or to rearrange linkage groups or whole chromosomes. The basic requirement for HDR is the presence of a homologous template; thus this process can be exploited for targeted integration of ectopic sequences into the plant genome. The development of different types of artificial site-specific nucleases allows for targeted DSB induction in the plant genome. Such synthetic nucleases have been used for both qualitatively studying DSB repair in vivo with respect to mechanistic differences and quantitatively in order to determine the role of key factors for NHEJ and HR, respectively. The conclusions drawn from these studies allow for a better understanding of genome evolution and help identifying synergistic or antagonistic genetic interactions while supporting biotechnological applications for transiently modifying the plant DNA repair machinery in favor of targeted genome engineering.
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Affiliation(s)
- Carla Schmidt
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michael Pacher
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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14
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Wolter F, Klemm J, Puchta H. Efficient in planta gene targeting in Arabidopsis using egg cell-specific expression of the Cas9 nuclease of Staphylococcus aureus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:735-746. [PMID: 29573495 DOI: 10.1111/tpj.13893] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/17/2018] [Accepted: 02/21/2018] [Indexed: 05/22/2023]
Abstract
Gene targeting (GT), the programmed change of genomic sequences by homologous recombination (HR), is still a major challenge in plants. We previously developed an in planta GT strategy by simultaneously releasing from the genome a dsDNA donor molecule and creating a double-stranded break (DSB) at a specific site within the targeted gene. Using Cas9 form Streptococcus pyogenes (SpCas9) under the control of a ubiquitin gene promoter, we obtained seeds harbouring GT events, although at a low frequency. In the present research we tested different developmentally controlled promotors and different kinds of DNA lesions for their ability to enhance GT of the acetolactate synthase (ALS) gene of Arabidopsis. For this purpose, we used Staphylococcus aureus Cas9 (SaCas9) nuclease and the SpCas9 nickase in various combinations. Thus, we analysed the effect of single-stranded break (SSB) activation of a targeted gene and/or the HR donor region. Moreover, we tested whether DSBs with 5' or 3' overhangs can improve in planta GT. Interestingly, the use of the SaCas9 nuclease controlled by an egg cell-specific promoter was the most efficient: depending on the line, in the very best case 6% of all seeds carried GT events. In a third of all lines, the targeting occurred around the 1% range of the tested seeds. Molecular analysis revealed that in about half of the cases perfect HR of both DSB ends occurred. Thus, using the improved technology, it should now be feasible to introduce any directed change into the Arabidopsis genome at will.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Jeannette Klemm
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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15
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True gene-targeting events by CRISPR/Cas-induced DSB repair of the PPO locus with an ectopically integrated repair template. Sci Rep 2018; 8:3338. [PMID: 29463822 PMCID: PMC5820285 DOI: 10.1038/s41598-018-21697-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/08/2018] [Indexed: 12/22/2022] Open
Abstract
In recent years, several tools have become available for improved gene-targeting (GT) in plants. DNA breaks at specific sites activate local DNA repair and recombination, including recombination with ectopic sequences leading to GT. Large-scale transformation with the repair template can be avoided by pre-insertion of the repair template in the genome and liberation by sequence-specific nucleases (in planta GT procedure). Here, we tested whether release of the repair template was required for GT. Plants were transformed with constructs encoding a CRISPR/Cas nuclease with a recognition site in the endogenous PPO gene and a repair template harboring a 5′ truncated PPO gene with two amino acid substitutions rendering the enzyme insensitive to the herbicide butafenacil. Selection resulted in so-called true GT events, repaired via homologous recombination at both ends of the gene and transmitted to the next generation. As the template was surrounded by geminiviral LIR sequences, we also tested whether replication of the template could be induced by crossing-in an integrated geminivirus REP gene. However, we could not find evidence for repair template replication by REP and we obtained similar numbers of GT events in these plants. Thus, GT is possible without any further processing of the pre-inserted repair template.
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16
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Rueppell O, Kuster R, Miller K, Fouks B, Rubio Correa S, Collazo J, Phaincharoen M, Tingek S, Koeniger N. A New Metazoan Recombination Rate Record and Consistently High Recombination Rates in the Honey Bee Genus Apis Accompanied by Frequent Inversions but Not Translocations. Genome Biol Evol 2018; 8:3653-3660. [PMID: 28173114 PMCID: PMC5521732 DOI: 10.1093/gbe/evw269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/31/2022] Open
Abstract
Western honey bees (Apis mellifera) far exceed the commonly observed 1–2 meiotic recombination events per chromosome and exhibit the highest Metazoan recombination rate (20 cM/Mb) described thus far. However, the reasons for this exceptional rate of recombination are not sufficiently understood. In a comparative study, we report on the newly constructed genomic linkage maps of Apis florea and Apis dorsata that represent the two honey bee lineages without recombination rate estimates so far. Each linkage map was generated de novo, based on SNP genotypes of haploid male offspring of a single female. The A. florea map spans 4,782 cM with 1,279 markers in 16 linkage groups. The A. dorsata map is 5,762 cM long and contains 1,189 markers in 16 linkage groups. Respectively, these map sizes result in average recombination rate estimates of 20.8 and 25.1 cM/Mb. Synteny analyses indicate that frequent intra-chromosomal rearrangements but no translocations among chromosomes accompany the high rates of recombination during the independent evolution of the three major honey bee lineages. Our results imply a common cause for the evolution of very high recombination rates in Apis. Our findings also suggest that frequent homologous recombination during meiosis might increase ectopic recombination and rearrangements within but not between chromosomes. It remains to be investigated whether the resulting inversions may have been important in the evolutionary differentiation between honey bee species.
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Affiliation(s)
- Olav Rueppell
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Ryan Kuster
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Katelyn Miller
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Bertrand Fouks
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Sara Rubio Correa
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Juan Collazo
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Mananya Phaincharoen
- Ratchaburi Campus, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Salim Tingek
- Agricultural Research Station, Tenom, Sabah, Malaysia
| | - Nikolaus Koeniger
- Molecular Ecology, Institute of Biology/Zoology, Martin-Luther-University Halle-Wittenberg, Halle an der Saale, Germany
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17
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Targeted recombination between homologous chromosomes for precise breeding in tomato. Nat Commun 2017; 8:15605. [PMID: 28548094 PMCID: PMC5458649 DOI: 10.1038/ncomms15605] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/05/2017] [Indexed: 01/10/2023] Open
Abstract
Homologous recombination (HR) between parental chromosomes occurs stochastically. Here, we report on targeted recombination between homologous chromosomes upon somatic induction of DNA double-strand breaks (DSBs) via CRISPR-Cas9. We demonstrate this via a visual and molecular assay whereby DSB induction between two alleles carrying different mutations in the PHYTOENE SYNTHASE (PSY1) gene results in yellow fruits with wild type red sectors forming via HR-mediated DSB repair. We also show that in heterozygote plants containing one psy1 allele immune and one sensitive to CRISPR, repair of the broken allele using the unbroken allele sequence template is a common outcome. In another assay, we show evidence of a somatically induced DSB in a cross between a psy1 edible tomato mutant and wild type Solanum pimpinellifolium, targeting only the S. pimpinellifolium allele. This enables characterization of germinally transmitted targeted somatic HR events, demonstrating that somatically induced DSBs can be exploited for precise breeding of crops. Targeted homologous recombination between parental chromosomes could facilitate precision breeding of crop plants. Here, Filler Hayut et al. show that CRISPR-Cas9 can be used to induce DNA double strand breaks in somatic tissue and achieve targeted recombination between homologs at an endogenous locus in tomato.
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18
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Paul JW, Qi Y. CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects. PLANT CELL REPORTS 2016; 35:1417-27. [PMID: 27114166 DOI: 10.1007/s00299-016-1985-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/12/2016] [Indexed: 05/20/2023]
Abstract
The increasing burden of the world population on agriculture requires the development of more robust crops. Dissecting the basic biology that underlies plant development and stress responses will inform the design of better crops. One powerful tool for studying plants at the molecular level is the RNA-programmed genome editing system composed of a clustered regularly interspaced short palindromic repeats (CRISPR)-encoded guide RNA and the nuclease Cas9. Here, some of the recent advances in CRISPR/Cas9 technology that have profound implications for improving the study of plant biology are described. These tools are also paving the way towards new horizons for biotechnologies and crop development.
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Affiliation(s)
- Joseph W Paul
- Department of Biology, Thomas Harriot College of Arts and Sciences, East Carolina University, Greenville, NC, 27858, USA
| | - Yiping Qi
- Department of Biology, Thomas Harriot College of Arts and Sciences, East Carolina University, Greenville, NC, 27858, USA.
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19
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Noman A, Aqeel M, He S. CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing. FRONTIERS IN PLANT SCIENCE 2016; 7:1740. [PMID: 27917188 PMCID: PMC5116475 DOI: 10.3389/fpls.2016.01740] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/04/2016] [Indexed: 05/07/2023]
Abstract
Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species. With approximate completion of conceptual work about CRISPR-Cas9, plant scientists are applying this genome editing tool for crop attributes enhancement. The capability of this system for performing targeted and efficient modifications in genome sequence as well as gene expression will certainly spur novel developments not only in model plants but in crop and ornamental plants as well. Additionally, due to non-involvement of foreign DNA, this technique may help alleviating regulatory issues associated with genetically modified plants. We expect that prevailing challenges in plant science like genomic region manipulation, crop specific vectors etc. will be addressed along with sustained growth of this genome editing tool. In this review, recent progress of CRISPR-Cas9 technology in plants has been summarized and discussed. We reviewed significance of CRISPR-Cas9 for specific and non-traditional aspects of plant life. It also covers strengths of this technique in comparison with other genome editing techniques, e.g., Zinc finger nucleases, Transcription activator-like effector nucleases and potential challenges in coming decades have been described.
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Affiliation(s)
- Ali Noman
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muhammad Aqeel
- Department of Botany, University of AgricultureFaisalabad, Pakistan
| | - Shuilin He
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- National Education Minister Key Laboratory for Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Shuilin He,
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20
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Knoll A, Fauser F, Puchta H. DNA recombination in somatic plant cells: mechanisms and evolutionary consequences. Chromosome Res 2015; 22:191-201. [PMID: 24788060 DOI: 10.1007/s10577-014-9415-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In somatic cells, recombination is a means of DNA damage repair. The most severe type of damage in nuclear DNA is double-strand breaks (DSBs) which may be repaired via either non-homologous end joining (NHEJ) or homologous recombination (HR). In this review, we will summarize the basic features, the mechanisms, and the key players of both repair modes in plants with a focus on the model plant Arabidopsis thaliana. NHEJ may result in insertion of sequences from elsewhere in the genome but is much more often associated with deletions. If more than one DSB is processed simultaneously via NHEJ, besides deletions, inversions or translocations may also arise. As the germ line is only set aside late in plant development, somatic changes may be transferred to the next generation. Thus, NHEJ might influence the evolution of plant genomes and indeed seems to be an important factor of genome shrinking. Deletions may also be due to DSB-induced recombination between tandem duplicated homologous sequences by single-strand annealing (SSA). Moreover, conservative HR using the synthesis-dependent strand annealing (SDSA) mechanism operates in somatic plant cells. The efficiency of SDSA is dependent on the genomic template used as matrix for the repair of the DSB. Besides DSBs, stalled replication forks may also be processed via HR. Several DNA processing enzymes are involved in the regulation of replication initiated HR, mostly in its suppression, and we summarize the current knowledge of these processes in plants.
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Affiliation(s)
- Alexander Knoll
- Karlsruhe Institute of Technology, Botanical Institute II, Hertzstr. 16, 76187, Karlsruhe, Germany
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21
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Puchta H, Fauser F. Synthetic nucleases for genome engineering in plants: prospects for a bright future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:727-41. [PMID: 24112784 DOI: 10.1111/tpj.12338] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/13/2013] [Accepted: 09/19/2013] [Indexed: 05/20/2023]
Abstract
By inducing double-strand breaks (DSB), it is possible to initiate DNA recombination. For a long time, it was not possible to use DSB induction for efficient genome engineering due to the lack of a means to target DSBs to specific sites. This limitation was overcome by development of modified meganucleases and synthetic DNA-binding domains. Domains derived from zinc-finger transcription factors or transcription activator-like effectors may be designed to recognize almost any DNA sequence. By fusing these domains to the endonuclease domains of a class II restriction enzyme, an active endonuclease dimer may be formed that introduces a site-specific DSB. Recent studies demonstrate that gene knockouts via non-homologous end joining or gene modification via homologous recombination are becoming routine in many plant species. By creating a single genomic DSB, complete knockout of a gene, sequence-specific integration of foreign DNA or subtle modification of individual amino acids in a specific protein domain may be achieved. The induction of two or more DSBs allows complex genomic rearrangements such as deletions, inversions or the exchange of chromosome arms. The potential for controlled genome engineering in plants is tremendous. The recently discovered RNA-based CRISPR/Cas system, a new tool to induce multiple DSBs, and sophisticated technical applications, such as the in planta gene targeting system, are further steps in this development. At present, the focus remains on engineering of single genes; in the future, engineering of whole genomes will become an option.
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Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, PO Box 6980, Karlsruhe, 76049, Germany
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22
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Vu GTH, Cao HX, Watanabe K, Hensel G, Blattner FR, Kumlehn J, Schubert I. Repair of Site-Specific DNA Double-Strand Breaks in Barley Occurs via Diverse Pathways Primarily Involving the Sister Chromatid. THE PLANT CELL 2014; 26:2156-2167. [PMID: 24876253 PMCID: PMC4079375 DOI: 10.1105/tpc.114.126607] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 05/18/2023]
Abstract
DNA double-strand break (DSB) repair mechanisms differ in their requirements for a homologous repair template and in the accuracy of the result. We aimed to quantify the outcome of repair of a single targeted DSB in somatic cells of young barley (Hordeum vulgare) plants. Amplicon sequencing of three reporter constructs revealed 47 to 58% of reads as repaired via nonhomologous end-joining (NHEJ) with deletions and/or small (1 to 3 bp) insertions. Alternative NHEJ revealed 2 to 5 bp microhomology (15.7% of cases) or new replication-mediated short duplications at sealed breaks. Although deletions outweigh insertions in barley, this bias was less pronounced and deleted sequences were shorter than in Arabidopsis thaliana. Between 17 and 33% of reads likely represent restoration of the original sequence. Depending on the construct, 20 to 33% of reads arose via gene conversion (homologous recombination). Remarkably, <1 to >8% of reads apparently display synthesis-dependent strand annealing linked with NHEJ, inserting 4 to 61 bp, mostly originating from the surrounding of breakpoints. Positional coincidence of >81% of sister chromatid exchanges with target loci is unprecedented for higher eukaryotes and indicates that most repair events for staggered DSBs, at least in barley, involve the sister chromatid and occur during S or G2 phase of the cell cycle.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany Faculty of Science and Central European Institute of Technology, Masaryk University, CZ-61137 Brno, Czech Republic
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23
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Shimatani Z, Nishizawa-Yokoi A, Endo M, Toki S, Terada R. Positive-negative-selection-mediated gene targeting in rice. FRONTIERS IN PLANT SCIENCE 2014; 5:748. [PMID: 25601872 PMCID: PMC4283509 DOI: 10.3389/fpls.2014.00748] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 12/08/2014] [Indexed: 05/04/2023]
Abstract
Gene targeting (GT) refers to the designed modification of genomic sequence(s) through homologous recombination (HR). GT is a powerful tool both for the study of gene function and for molecular breeding. However, in transformation of higher plants, non-homologous end joining (NHEJ) occurs overwhelmingly in somatic cells, masking HR-mediated GT. Positive-negative selection (PNS) is an approach for finding HR-mediated GT events because it can eliminate NHEJ effectively by expression of a negative-selection marker gene. In rice-a major crop worldwide-reproducible PNS-mediated GT of endogenous genes has now been successfully achieved. The procedure is based on strong PNS using diphtheria toxin A-fragment as a negative marker, and has succeeded in the directed modification of several endogenous rice genes in various ways. In addition to gene knock-outs and knock-ins, a nucleotide substitution in a target gene was also achieved recently. This review presents a summary of the development of the rice PNS system, highlighting its advantages. Different types of gene modification and gene editing aimed at developing new plant breeding technology based on PNS are discussed.
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Affiliation(s)
- Zenpei Shimatani
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Ayako Nishizawa-Yokoi
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Masaki Endo
- 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
| | - Rie Terada
- Development of Agrobiological Resources, Faculty of Agriculture, Meijo UniversityNagoya, Japan
- *Correspondence: Rie Terada, Development of Agrobiological Resources, Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya 468-8502, Aichi, Japan e-mail:
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24
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White RR, Sung P, Vestal CG, Benedetto G, Cornelio N, Richardson C. Double-strand break repair by interchromosomal recombination: an in vivo repair mechanism utilized by multiple somatic tissues in mammals. PLoS One 2013; 8:e84379. [PMID: 24349572 PMCID: PMC3862804 DOI: 10.1371/journal.pone.0084379] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 11/22/2013] [Indexed: 01/22/2023] Open
Abstract
Homologous recombination (HR) is essential for accurate genome duplication and maintenance of genome stability. In eukaryotes, chromosomal double strand breaks (DSBs) are central to HR during specialized developmental programs of meiosis and antigen receptor gene rearrangements, and form at unusual DNA structures and stalled replication forks. DSBs also result from exposure to ionizing radiation, reactive oxygen species, some anti-cancer agents, or inhibitors of topoisomerase II. Literature predicts that repair of such breaks normally will occur by non-homologous end-joining (in G1), intrachromosomal HR (all phases), or sister chromatid HR (in S/G2). However, no in vivo model is in place to directly determine the potential for DSB repair in somatic cells of mammals to occur by HR between repeated sequences on heterologs (i.e., interchromosomal HR). To test this, we developed a mouse model with three transgenes—two nonfunctional green fluorescent protein (GFP) transgenes each containing a recognition site for the I-SceI endonuclease, and a tetracycline-inducible I-SceI endonuclease transgene. If interchromosomal HR can be utilized for DSB repair in somatic cells, then I-SceI expression and induction of DSBs within the GFP reporters may result in a functional GFP+ gene. Strikingly, GFP+ recombinant cells were observed in multiple organs with highest numbers in thymus, kidney, and lung. Additionally, bone marrow cultures demonstrated interchromosomal HR within multiple hematopoietic subpopulations including multi-lineage colony forming unit–granulocyte-erythrocyte-monocyte-megakaryocte (CFU-GEMM) colonies. This is a direct demonstration that somatic cells in vivo search genome-wide for homologous sequences suitable for DSB repair, and this type of repair can occur within early developmental populations capable of multi-lineage differentiation.
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Affiliation(s)
- Ryan R. White
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Patricia Sung
- Developmental Biology, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - C. Greer Vestal
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Gregory Benedetto
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Noelle Cornelio
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Christine Richardson
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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Ayar A, Wehrkamp-Richter S, Laffaire JB, Le Goff S, Levy J, Chaignon S, Salmi H, Lepicard A, Sallaud C, Gallego ME, White CI, Paul W. Gene targeting in maize by somatic ectopic recombination. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:305-14. [PMID: 23094946 DOI: 10.1111/pbi.12014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/28/2012] [Accepted: 09/25/2012] [Indexed: 05/20/2023]
Abstract
Low transformation efficiency and high background of non-targeted events are major constraints to gene targeting in plants. We demonstrate here applicability in maize of a system that reduces the constraint from transformation efficiency. The system requires regenerable transformants in which all of the following elements are stably integrated in the genome: (i) donor DNA with the gene of interest adjacent to sequence for repair of a defective selectable marker, (ii) sequence encoding a rare-cutting endonuclease such as I-SceI, (iii) a target locus (TL) comprising the defective selectable marker and I-SceI cleavage site. Typically, this requires additional markers for the integration of the donor and target sequences, which may be assembled through cross-pollination of separate transformants. Inducible expression of I-SceI then cleaves the TL and facilitates homologous recombination, which is assayed by selection for the repaired marker. We used bar and gfp markers to identify assembled transformants, a dexamethasone-inducible I-SceI::GR protein, and selection for recombination events that restored an intact nptII. Applying this strategy to callus permitted the selection of recombination into the TL at a frequency of 0.085% per extracted immature embryo (29% of recombinants). Our results also indicate that excision of the donor locus (DL) through the use of flanking I-SceI cleavage sites may be unnecessary, and a source of unwanted repair events at the DL. The system allows production, from each assembled transformant, of many cells that subsequently can be treated to induce gene targeting. This may facilitate gene targeting in plant species for which transformation efficiencies are otherwise limiting.
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Affiliation(s)
- Ayhan Ayar
- Biogemma, Centre de Recherche de Chappes, Chappes, France
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26
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Qi Y, Zhang Y, Zhang F, Baller JA, Cleland SC, Ryu Y, Starker CG, Voytas DF. Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways. Genome Res 2013; 23:547-54. [PMID: 23282329 PMCID: PMC3589543 DOI: 10.1101/gr.145557.112] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Improved methods for engineering sequence-specific nucleases, including zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs), have made it possible to precisely modify plant genomes. However, the success of genome modification is largely dependent on the intrinsic activity of the engineered nucleases. In this study, we sought to enhance ZFN-mediated targeted mutagenesis and gene targeting (GT) in Arabidopsis by manipulating DNA repair pathways. Using a ZFN that creates a double-strand break (DSB) at the endogenous ADH1 locus, we analyzed repair outcomes in the absence of DNA repair proteins such as KU70 and LIG4 (both involved in classic nonhomologous end-joining, NHEJ) and SMC6B (involved in sister-chromatid-based homologous recombination, HR). We achieved a fivefold to 16-fold enhancement in HR-based GT in a ku70 mutant and a threefold to fourfold enhancement in GT in the lig4 mutant. Although the NHEJ mutagenesis frequency was not significantly changed in ku70 or lig4, DNA repair was shifted to microhomology-dependent alternative NHEJ. As a result, mutations in both ku70 and lig4 were predominantly large deletions, which facilitates easy screening for mutations by PCR. Interestingly, NHEJ mutagenesis and GT at the ADH1 locus were enhanced by sixfold to eightfold and threefold to fourfold, respectively, in a smc6b mutant. The increase in NHEJ-mediated mutagenesis by loss of SMC6B was further confirmed using ZFNs that target two other Arabidopsis genes, namely, TT4 and MPK8. Considering that components of DNA repair pathways are highly conserved across species, mutations in DNA repair genes likely provide a universal strategy for harnessing repair pathways to achieve desired targeted genome modifications.
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Affiliation(s)
- Yiping Qi
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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27
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Abstract
Recent advances in genome engineering provide newfound control over a plant's genetic material. It is now possible for most bench scientists to alter DNA in living plant cells in a variety of ways, including introducing specific nucleotide substitutions in a gene that change a protein's amino acid sequence, deleting genes or chromosomal segments, and inserting foreign DNA at precise genomic locations. Such targeted DNA sequence modifications are enabled by sequence-specific nucleases that create double-strand breaks in the genomic loci to be altered. The repair of the breaks, through either homologous recombination or nonhomologous end joining, can be controlled to achieve the desired sequence modification. Genome engineering promises to advance basic plant research by linking DNA sequences to biological function. Further, genome engineering will enable plants' biosynthetic capacity to be harnessed to produce the many agricultural products required by an expanding world population.
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Affiliation(s)
- Daniel F Voytas
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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28
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Weber N, Halpin C, Hannah LC, Jez JM, Kough J, Parrott W. Editor's choice: Crop genome plasticity and its relevance to food and feed safety of genetically engineered breeding stacks. PLANT PHYSIOLOGY 2012; 160:1842-53. [PMID: 23060369 PMCID: PMC3510115 DOI: 10.1104/pp.112.204271] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/02/2012] [Indexed: 05/22/2023]
Affiliation(s)
- Natalie Weber
- Pioneer Hi-Bred International, Wilmington, Delaware 19880, USA
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29
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Liu R, Koyanagi KO, Chen S, Kishima Y. Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: lessons from endogenous pararetrovirus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:817-28. [PMID: 22900922 DOI: 10.1111/tpj.12002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In plant genomes, the incorporation of DNA segments is not a common method of artificial gene transfer. Nevertheless, various segments of pararetroviruses have been found in plant genomes in recent decades. The rice genome contains a number of segments of endogenous rice tungro bacilliform virus-like sequences (ERTBVs), many of which are present between AT dinucleotide repeats (ATrs). Comparison of genomic sequences between two closely related rice subspecies, japonica and indica, allowed us to verify the preferential insertion of ERTBVs into ATrs. In addition to ERTBVs, the comparative analyses showed that ATrs occasionally incorporate repeat sequences including transposable elements, and a wide range of other sequences. Besides the known genomic sequences, the insertion sequences also represented DNAs of unclear origins together with ERTBVs, suggesting that ATrs have integrated episomal DNAs that would have been suspended in the nucleus. Such insertion DNAs might be trapped by ATrs in the genome in a host-dependent manner. Conversely, other simple mono- and dinucleotide sequence repeats (SSR) were less frequently involved in insertion events relative to ATrs. Therefore, ATrs could be regarded as hot spots of double-strand breaks that induce non-homologous end joining. The insertions within ATrs occasionally generated new gene-related sequences or involved structural modifications of existing genes. Likewise, in a comparison between Arabidopsis thaliana and Arabidopsis lyrata, the insertions preferred ATrs to other SSRs. Therefore ATrs in plant genomes could be considered as genomic dumping sites that have trapped various DNA molecules and may have exerted a powerful evolutionary force.
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Affiliation(s)
- Ruifang Liu
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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30
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Waterworth WM, Drury GE, Bray CM, West CE. Repairing breaks in the plant genome: the importance of keeping it together. THE NEW PHYTOLOGIST 2011; 192:805-822. [PMID: 21988671 DOI: 10.1111/j.1469-8137.2011.03926.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA damage threatens the integrity of the genome and has potentially lethal consequences for the organism. Plant DNA is under continuous assault from endogenous and environmental factors and effective detection and repair of DNA damage are essential to ensure the stability of the genome. One of the most cytotoxic forms of DNA damage are DNA double-strand breaks (DSBs) which fragment chromosomes. Failure to repair DSBs results in loss of large amounts of genetic information which, following cell division, severely compromises daughter cells that receive fragmented chromosomes. This review will survey recent advances in our understanding of plant responses to chromosomal breaks, including the sources of DNA damage, the detection and signalling of DSBs, mechanisms of DSB repair, the role of chromatin structure in repair, DNA damage signalling and the link between plant recombination pathways and transgene integration. These mechanisms are of critical importance for maintenance of plant genome stability and integrity under stress conditions and provide potential targets for the improvement of crop plants both for stress resistance and for increased precision in the generation of genetically improved varieties.
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Affiliation(s)
| | - Georgina E Drury
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Clifford M Bray
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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31
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Mannuss A, Trapp O, Puchta H. Gene regulation in response to DNA damage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:154-65. [PMID: 21867786 DOI: 10.1016/j.bbagrm.2011.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/25/2011] [Accepted: 08/04/2011] [Indexed: 11/17/2022]
Abstract
To deal with different kinds of DNA damages, there are a number of repair pathways that must be carefully orchestrated to guarantee genomic stability. Many proteins that play a role in DNA repair are involved in multiple pathways and need to be tightly regulated to conduct the functions required for efficient repair of different DNA damage types, such as double strand breaks or DNA crosslinks caused by radiation or genotoxins. While most of the factors involved in DNA repair are conserved throughout the different kingdoms, recent results have shown that the regulation of their expression is variable between different organisms. In the following paper, we give an overview of what is currently known about regulating factors and gene expression in response to DNA damage and put this knowledge in context with the different DNA repair pathways in plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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Affiliation(s)
- Anja Mannuss
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Böhmdorfer G, Schleiffer A, Brunmeir R, Ferscha S, Nizhynska V, Kozák J, Angelis KJ, Kreil DP, Schweizer D. GMI1, a structural-maintenance-of-chromosomes-hinge domain-containing protein, is involved in somatic homologous recombination in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:420-33. [PMID: 21481027 DOI: 10.1111/j.1365-313x.2011.04604.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA double-strand breaks (DSBs) pose one of the most severe threats to genome integrity, potentially leading to cell death. After detection of a DSB, the DNA damage and repair response is initiated and the DSB is repaired by non-homologous end joining and/or homologous recombination. Many components of these processes are still unknown in Arabidopsis thaliana. In this work, we characterized γ-irradiation and mitomycin C induced 1 (GMI1), a member of the SMC-hinge domain-containing protein family. RT-PCR analysis and promoter-GUS fusion studies showed that γ-irradiation, the radio-mimetic drug bleocin, and the DNA cross-linking agent mitomycin C strongly enhance GMI1 expression particularly in meristematic tissues. The induction of GMI1 by γ-irradiation depends on the signalling kinase Ataxia telangiectasia-mutated (ATM) but not on ATM and Rad3-related (ATR). Epistasis analysis of single and double mutants demonstrated that ATM acts upstream of GMI1 while the atr gmi1-2 double mutant was more sensitive than the respective single mutants. Comet assay revealed a reduced rate of DNA double-strand break repair in gmi1 mutants during the early recovery phase after exposure to bleocin. Moreover, the rate of homologous recombination of a reporter construct was strongly reduced in gmi1 mutant plants upon exposure to bleocin or mitomycin C. GMI1 is the first member of its protein family known to be involved in DNA repair.
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MESH Headings
- Arabidopsis/drug effects
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis/radiation effects
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Chromosomes, Plant/metabolism
- Cloning, Molecular
- Comet Assay
- DNA Breaks, Double-Stranded
- DNA Repair
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Flowers/drug effects
- Flowers/metabolism
- Flowers/radiation effects
- Gene Expression Regulation, Plant
- Gene Fusion
- Meristem/drug effects
- Meristem/metabolism
- Meristem/radiation effects
- Microarray Analysis
- Mitomycin/pharmacology
- Mutagenesis, Insertional
- Recombination, Genetic
- Reverse Transcriptase Polymerase Chain Reaction
- Seedlings/drug effects
- Seedlings/genetics
- Transcription, Genetic
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Affiliation(s)
- Gudrun Böhmdorfer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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33
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Abstract
Homologous recombination (HR) is a central cellular process involved in many aspects of genome maintenance such as DNA repair, replication, telomere maintenance, and meiotic chromosomal segregation. HR is highly conserved among eukaryotes, contributing to genome stability as well as to the generation of genetic diversity. It has been intensively studied, for almost a century, in plants and in other organisms. In this antireview, rather than reviewing existing knowledge, we wish to underline the many open questions in plant HR. We will discuss the following issues: how do we define homology and how the degree of homology affects HR? Are there any plant-specific HR qualities, how extensive is functional conservation and did HR proteins acquire new functions? How efficient is HR in plants and what are the cis and the trans factors that regulate it? Finally, we will give the prospects for enhancing the rates of gene targeting and meiotic HR for plant breeding purposes.
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34
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Yang Z, Tang L, Li M, Chen L, Xu J, Wu G, Li H. Monitoring homologous recombination in rice (Oryza sativa L.). Mutat Res 2010; 691:55-63. [PMID: 20670635 DOI: 10.1016/j.mrfmmm.2010.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 04/11/2010] [Accepted: 07/09/2010] [Indexed: 05/29/2023]
Abstract
Here we describe a system to assay homologous recombination during the complete life cycle of rice (Oryza sativa L.). Rice plants were transformed with two copies of non-functional GUS reporter overlap fragments as recombination substrate. Recombination was observed in all plant organs examined, from the seed stage until the flowering stage of somatic plant development. Embryogenic cells exhibited the highest recombination ability with an average of 3x10(-5) recombination events per genome, which is about 10-fold of that observed in root cells, and two orders of that observed in leaf cells. Histological analysis revealed that recombination events occurred in diverse cell types, but preferentially in cells with small size. Examples of this included embryogenic cells in callus, phloem cells in the leaf vein, and cells located in the root apical meristem. Steady state RNA analysis revealed that the expression levels of rice Rad51 homologs are positively correlated with increased recombination rates in embryogenic calli, roots and anthers. Finally, radiation treatment of plantlets from distinct recombination lines increased the recombination frequency to different extents. These results showed that homologous recombination frequency can be effectively measured in rice using a transgene reporter assay. This system will facilitate the study of DNA damage signaling and homologous recombination in rice, a model monocot.
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Affiliation(s)
- Zhuanying Yang
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
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35
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Gaeta RT, Chris Pires J. Homoeologous recombination in allopolyploids: the polyploid ratchet. THE NEW PHYTOLOGIST 2010; 186:18-28. [PMID: 20002315 DOI: 10.1111/j.1469-8137.2009.03089.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidization and recombination are two important processes driving evolution through the building and reshaping of genomes. Allopolyploids arise from hybridization and chromosome doubling among distinct, yet related species. Polyploids may display novel variation relative to their progenitors, and the sources of this variation lie not only in the acquisition of extra gene dosages, but also in the genomic changes that occur after divergent genomes unite. Genomic changes (deletions, duplications, and translocations) have been detected in both recently formed natural polyploids and resynthesized polyploids. In resynthesized Brassica napus allopolyploids, there is evidence that many genetic changes are the consequence of homoeologous recombination. Homoeologous recombination can generate novel gene combinations and phenotypes, but may also destabilize the karyotype and lead to aberrant meiotic behavior and reduced fertility. Thus, natural selection plays a role in the establishment and maintenance of fertile natural allopolyploids that have stabilized chromosome inheritance and a few advantageous chromosomal rearrangements. We discuss the evidence for genome rearrangements that result from homoeologous recombination in resynthesized B. napus and how these observations may inform phenomena such as chromosome replacement, aneuploidy, non-reciprocal translocations and gene conversion seen in other polyploids.
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Affiliation(s)
- Robert T Gaeta
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7310, USA
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36
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Blanck S, Kobbe D, Hartung F, Fengler K, Focke M, Puchta H. A SRS2 homolog from Arabidopsis thaliana disrupts recombinogenic DNA intermediates and facilitates single strand annealing. Nucleic Acids Res 2010; 37:7163-76. [PMID: 19767619 PMCID: PMC2790887 DOI: 10.1093/nar/gkp753] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic and biochemical analyses of SRS2 homologs in fungi indicate a function in the processing of homologous recombination (HR) intermediates. To date, no SRS2 homologs have been described and analyzed in higher eukaryotes. Here, we report the first biochemical characterization of an SRS2 homolog from a multicellular eukaryote, the plant Arabidopsis thaliana. We studied the basic properties of AtSRS2 and were able to show that it is a functional 3'- to 5'-helicase. Furthermore, we characterized its biochemical function on recombinogenic intermediates and were able to show the unwinding of nicked Holliday junctions (HJs) and partial HJs (PX junctions). For the first time, we demonstrated strand annealing activity for an SRS2 homolog and characterized its strand pairing activity in detail. Our results indicate that AtSRS2 has properties that enable it to be involved in different steps during the processing of recombination intermediates. On the one hand, it could be involved in the unwinding of an elongating invading strand from a donor strand, while on the other hand, it could be involved in the annealing of the elongated strand at a later step.
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Affiliation(s)
- Sandra Blanck
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76128 Karlsruhe, Germany
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37
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Abstract
DNA chromosomal DSBs (double-strand breaks) are potentially hazardous DNA lesions, and their accurate repair is essential for the successful maintenance and propagation of genetic information. Two major pathways have evolved to repair DSBs: HR (homologous recombination) and NHEJ (non-homologous end-joining). Depending on the context in which the break is encountered, HR and NHEJ may either compete or co-operate to fix DSBs in eukaryotic cells. Defects in either pathway are strongly associated with human disease, including immunodeficiency and cancer predisposition. Here we review the current knowledge of how NHEJ and HR are controlled in somatic mammalian cells, and discuss the role of the chromatin context in regulating each pathway. We also review evidence for both co-operation and competition between the two pathways.
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38
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Watanabe K, Pacher M, Dukowic S, Schubert V, Puchta H, Schubert I. The STRUCTURAL MAINTENANCE OF CHROMOSOMES 5/6 complex promotes sister chromatid alignment and homologous recombination after DNA damage in Arabidopsis thaliana. THE PLANT CELL 2009; 21:2688-99. [PMID: 19737979 PMCID: PMC2768936 DOI: 10.1105/tpc.108.060525] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/13/2009] [Accepted: 08/24/2009] [Indexed: 05/18/2023]
Abstract
Sister chromatids are often arranged as incompletely aligned entities in interphase nuclei of Arabidopsis thaliana. The STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC) 5/6 complex, together with cohesin, is involved in double-strand break (DSB) repair by sister chromatid recombination in yeasts and mammals. Here, we analyzed the function of genes in Arabidopsis. The wild-type allele of SMC5 is essential for seed development. Each of the two SMC6 homologs of Arabidopsis is required for efficient repair of DNA breakage via intermolecular homologous recombination in somatic cells. Alignment of sister chromatids is enhanced transiently after X-irradiation (and mitomycin C treatment) in wild-type nuclei. In the smc5/6 mutants, the x-ray-mediated increase in sister chromatid alignment is much lower and delayed. The reduced S phase-established cohesion caused by a knockout mutation in one of the alpha-kleisin genes, SYN1, also perturbed enhancement of sister chromatid alignment after irradiation, suggesting that the S phase-established cohesion is a prerequisite for correct DSB-dependent cohesion. The radiation-sensitive51 mutant, deficient in heteroduplex formation during DSB repair, showed wild-type frequencies of sister chromatid alignment after X-irradiation, implying that the irradiation-mediated increase in sister chromatid alignment is a prerequisite for, rather than a consequence of, DNA strand exchange between sister chromatids. Our results suggest that the SMC5/6 complex promotes sister chromatid cohesion after DNA breakage and facilitates homologous recombination between sister chromatids.
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Affiliation(s)
- Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Michael Pacher
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Stefanie Dukowic
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Holger Puchta
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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Roger E, Grunau C, Pierce RJ, Hirai H, Gourbal B, Galinier R, Emans R, Cesari IM, Cosseau C, Mitta G. Controlled chaos of polymorphic mucins in a metazoan parasite (Schistosoma mansoni) interacting with its invertebrate host (Biomphalaria glabrata). PLoS Negl Trop Dis 2008; 2:e330. [PMID: 19002242 PMCID: PMC2576457 DOI: 10.1371/journal.pntd.0000330] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/10/2008] [Indexed: 01/21/2023] Open
Abstract
Invertebrates were long thought to possess only a simple, effective and hence non-adaptive defence system against microbial and parasitic attacks. However, recent studies have shown that invertebrate immunity also relies on immune receptors that diversify (e.g. in echinoderms, insects and mollusks (Biomphalaria glabrata)). Apparently, individual or population-based polymorphism-generating mechanisms exists that permit the survival of invertebrate species exposed to parasites. Consequently, the generally accepted arms race hypothesis predicts that molecular diversity and polymorphism also exist in parasites of invertebrates. We investigated the diversity and polymorphism of parasite molecules (Schistosoma mansoni Polymorphic Mucins, SmPoMucs) that are key factors for the compatibility of schistosomes interacting with their host, the mollusc Biomphalaria glabrata. We have elucidated the complex cascade of mechanisms acting both at the genomic level and during expression that confer polymorphism to SmPoMuc. We show that SmPoMuc is coded by a multi-gene family whose members frequently recombine. We show that these genes are transcribed in an individual-specific manner, and that for each gene, multiple splice variants exist. Finally, we reveal the impact of this polymorphism on the SmPoMuc glycosylation status. Our data support the view that S. mansoni has evolved a complex hierarchical system that efficiently generates a high degree of polymorphism—a “controlled chaos”—based on a relatively low number of genes. This contrasts with protozoan parasites that generate antigenic variation from large sets of genes such as Trypanosoma cruzi, Trypanosoma brucei and Plasmodium falciparum. Our data support the view that the interaction between parasites and their invertebrate hosts are far more complex than previously thought. While most studies in this matter have focused on invertebrate host diversification, we clearly show that diversifying mechanisms also exist on the parasite side of the interaction. Our findings shed new light on how and why invertebrate immunity develops. Contrary to the traditional view that immunity in invertebrates is limited to non-specific mechanisms, recent studies have shown that they have diverse, specific immune receptors. An example is provided by the FREPs of the mollusk Biomphalaria glabrata, polymorphic members of the immunoglobulin superfamily. This capacity for an individual or population-based polymorphic immune response raises the question of whether a corresponding polymorphism exists in parasites of invertebrates, as would be expected in an “arms race” between host and parasite. We have indeed identified such polymorphic molecules in Schistosoma mansoni, a flatworm parasite of B. glabrata, by comparing two strains of schistosome that are respectively compatible and incompatible with the same mollusk host strain. However, in contrast to antigenic variation in protozoan parasites that is based on an extensive gene repertoire, we show here that a high level of polymorphism in these S. mansoni polymorphic mucins (SmPoMucs) is generated from a low number of genes by a complex cascade of mechanisms, a “controlled chaos”.
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Affiliation(s)
- Emmanuel Roger
- Parasitologie Fonctionnelle et Evolutive, UMR 5244, CNRS Université de Perpignan, Perpignan, France
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40
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Pacher M, Schmidt-Puchta W, Puchta H. Two unlinked double-strand breaks can induce reciprocal exchanges in plant genomes via homologous recombination and nonhomologous end joining. Genetics 2007; 175:21-9. [PMID: 17057227 PMCID: PMC1775016 DOI: 10.1534/genetics.106.065185] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Accepted: 10/06/2006] [Indexed: 11/18/2022] Open
Abstract
Using the rare-cutting endonuclease I-SceI we were able to demonstrate before that the repair of a single double-strand break (DSB) in a plant genome can be mutagenic due to insertions and deletions. However, during replication or due to irradiation several breaks might be induced simultaneously. To analyze the mutagenic potential of such a situation we established an experimental system in tobacco harboring two unlinked transgenes, each carrying an I-SceI site. After transient expression of I-SceI a kanamycin-resistance marker could be restored by joining two previously unlinked broken ends, either by homologous recombination (HR) or by nonhomologous end joining (NHEJ). Indeed, we were able to recover HR and NHEJ events with similar frequencies. Despite the fact that no selection was applied for joining the two other ends, the respective linkage could be detected in most cases tested, demonstrating that the respective exchanges were reciprocal. The frequencies obtained indicate that DSB-induced translocation is up to two orders of magnitude more frequent in somatic cells than ectopic gene conversion. Thus, DSB-induced reciprocal exchanges might play a significant role in plant genome evolution. The technique applied in this study may also be useful for the controlled exchange of unlinked sequences in plant genomes.
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Affiliation(s)
- Michael Pacher
- Botany II, University of Karlsruhe, D-76128 Karlsruhe, Germany
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Kamisugi Y, Schlink K, Rensing SA, Schween G, von Stackelberg M, Cuming AC, Reski R, Cove DJ. The mechanism of gene targeting in Physcomitrella patens: homologous recombination, concatenation and multiple integration. Nucleic Acids Res 2006; 34:6205-14. [PMID: 17090599 PMCID: PMC1693892 DOI: 10.1093/nar/gkl832] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The model bryophyte Physcomitrella patens exhibits high frequencies of gene targeting when transformed with DNA constructs containing sequences homologous with genomic loci. ‘Targeted gene replacement’ (TGR) resulting from homologous recombination (HR) between each end of a targeting construct and the targeted locus occurs when either single or multiple targeting vectors are delivered. In the latter instance simultaneous, multiple, independent integration of different transgenes occurs at the targeted loci. In both single gene and ‘batch’ transformations, DNA can also be found to undergo ‘targeted insertion’ (TI), integrating at one end of the targeted locus by HR with one flanking sequence of the vector accompanied by an apparent non-homologous end-joining (NHEJ) event at the other. Untargeted integration at nonhomologous sites also occurs, but at a lower frequency. Molecular analysis of TI at a single locus shows that this occurs as a consequence of concatenation of the transforming DNA, in planta, prior to integration, followed by HR between a single site in the genomic target and two of its repeated homologues in the concatenated vector. This reinforces the view that HR is the major pathway by which transforming DNA is integrated in Physcomitrella.
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Affiliation(s)
- Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University LeedsLS2 9JT, UK
| | - Katja Schlink
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchaenzlestrasse 1, D-79104 Freiburg, Germany
- Forest Genetics, Department of Plant Sciences, Life Science Center Weihenstephan, Technische Universität MünchenAm Hochanger 13, D-85354 Freising, Germany
| | - Stefan A. Rensing
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Gabriele Schween
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Mark von Stackelberg
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Andrew C. Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University LeedsLS2 9JT, UK
- To whom correspondence should be addressed. Tel: +44 113 3433096; Fax: +44 113 3433144;
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchaenzlestrasse 1, D-79104 Freiburg, Germany
| | - David J. Cove
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University LeedsLS2 9JT, UK
- Department of Biology, Washington University in St LouisSt Louis, MO 63130-4899, USA
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42
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Affiliation(s)
- Seisuke Kimura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda-shi, Chiba, Japan
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43
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Bray CM, West CE. DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity. THE NEW PHYTOLOGIST 2005; 168:511-28. [PMID: 16313635 DOI: 10.1111/j.1469-8137.2005.01548.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As obligate phototrophs, plants harness energy from sunlight to split water, producing oxygen and reducing power. This lifestyle exposes plants to particularly high levels of genotoxic stress that threatens genomic integrity, leading to mutation, developmental arrest and cell death. Plants, which with algae are the only photosynthetic eukaryotes, have evolved very effective pathways for DNA damage signalling and repair, and this review summarises our current understanding of these processes in the responses of plants to genotoxic stress. We also identify how the use of new and emerging technologies can complement established physiological and ecological studies to progress the application of this knowledge in biotechnology.
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Affiliation(s)
- Clifford M Bray
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
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Cotsaftis O, Guiderdoni E. Enhancing gene targeting efficiency in higher plants: rice is on the move. Transgenic Res 2005; 14:1-14. [PMID: 15865044 DOI: 10.1007/s11248-004-4066-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Meeting the challenge of routine gene targeting (GT) in higher plants is of crucial interest to researchers and plant breeders who are currently in need of a powerful tool to specifically modify a given locus in a genome. Higher plants have long been considered the last lineage resistant to targeting technology. However, a recent report described an efficient method of T-DNA-mediated targeted disruption of a non-selectable locus in rice [Terada et al., Nat Biotechnol 20: 1030-1034 (2002)]. Though this study was an obvious breakthrough, further improvement of GT frequencies may derive from a better understanding of the natural mechanisms that control homologous recombination (HR) processes. In this review, we will focus on what is known about HR and the factors which may hamper the development of routine GT by HR in higher plants. We will also present the current strategies envisaged to overcome these limitations, such as expression of recombination proteins and refinements in the design of the transformation vector.
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Affiliation(s)
- Olivier Cotsaftis
- UMR1096 PIA, Biotrop Program, Cirad-Amis, Avenue Agropolis, F-34398 Montpellier Cedex 5, France.
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Opperman R, Emmanuel E, Levy AA. The effect of sequence divergence on recombination between direct repeats in Arabidopsis. Genetics 2005; 168:2207-15. [PMID: 15611187 PMCID: PMC1448723 DOI: 10.1534/genetics.104.032896] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well established that sequence divergence has an inhibitory effect on homologous recombination. However, a detailed analysis of this relationship is missing for most higher eukaryotes. We have measured the rate of somatic recombination between direct repeats as a function of the number, type, and position of divergent nucleotides in Arabidopsis. We show that a minor divergence level of 0.16% (one mutation in otherwise identical 618 bp) has a profound effect, decreasing the recombination rate approximately threefold. A further increase in the divergence level affects the recombination rate to a smaller extent until a "divergence saturation" effect is reached at relatively low levels of divergence ( approximately 0.5%). The type of mismatched nucleotide does not affect recombination rates. The decrease in the rate of recombination caused by a single mismatch was not affected by the position of the mismatch along the repeat. This suggests that most recombination intermediate tracts contain a mismatch and thus are as long as the full length of the 618-bp repeats. Finally, we could deduce an antirecombination efficiency of approximately 66% for the first mismatch in the repeat. Altogether, this work shows some degree of conservation across kingdoms when compared to previous reports in yeast; it also provides new insight into the effect of sequence divergence on homologous recombination.
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Affiliation(s)
- Roy Opperman
- Plant Sciences Department, Weizmann Institute of Science, Rehovot, 76100 Israel
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46
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Molinier J, Ries G, Bonhoeffer S, Hohn B. Interchromatid and interhomolog recombination in Arabidopsis thaliana. THE PLANT CELL 2004; 16:342-52. [PMID: 14729918 PMCID: PMC341908 DOI: 10.1105/tpc.019042] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Accepted: 12/03/2003] [Indexed: 05/18/2023]
Abstract
Intermolecular recombination events were monitored in Arabidopsis thaliana lines using specially designed recombination traps consisting of tandem disrupted beta-glucuronidase or luciferase reporter genes in direct repeat orientation. Recombination frequencies (RFs) varied between the different lines, indicating possible position effects influencing intermolecular recombination processes. The RFs between sister chromatids and between homologous chromosomes were measured in plants either hemizygous or homozygous for a transgene locus. The RFs in homozygous plants exceeded those of hemizygous plants by a factor of >2, implying that in somatic plant cells both sister chromatid recombination and recombination between homologous chromosomes exist for recombinational DNA repair. In addition, different DNA-damaging agents stimulated recombination in homozygous and hemizygous plants to different extents in a manner dependent on the type of DNA damage and on the genomic region. The genetic and molecular analysis of recombination events showed that most of the somatic recombination events result from gene conversion, although a pop-out event has also been characterized.
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Affiliation(s)
- Jean Molinier
- Friedrich Miescher Institute, CH-4058 Basel, Switzerland.
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Orel N, Kyryk A, Puchta H. Different pathways of homologous recombination are used for the repair of double-strand breaks within tandemly arranged sequences in the plant genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:604-12. [PMID: 12940953 DOI: 10.1046/j.1365-313x.2003.01832.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Different DNA repair pathways that use homologous sequences in close proximity to genomic double-strand breaks (DSBs) result in either an internal deletion or a gene conversion. We determined the efficiency of these pathways in somatic plant cells of transgenic Arabidopsis lines by monitoring the restoration of the beta-glucuronidase (GUS) marker gene. The transgenes contain a recognition site for the restriction endonuclease I-SceI either between direct GUS repeats to detect deletion formation (DGU.US), or within the GUS gene to detect gene conversion using a nearby donor sequence in direct or inverted orientation (DU.GUS and IU.GUS). Without expression of I-SceI, the frequency of homologous recombination (HR) was low and similar for all three constructs. By crossing the different lines with an I-SceI expressing line, DSB repair was induced, and resulted in one to two orders of magnitude higher recombination frequency. The frequencies obtained with the DGU.US construct were about five times higher than those obtained with DU.GUS and IU.GUS, irrespective of the orientation of the donor sequence. Our results indicate that recombination associated with deletions is the most efficient pathway of homologous DSB repair in plants. However, DSB-induced gene conversion seems to be frequent enough to play a significant role in the evolution of tandemly arranged gene families like resistance genes.
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Affiliation(s)
- Nadiya Orel
- Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, D-06466 Gatersleben, Germany
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48
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Hohe A, Reski R. A tool for understanding homologous recombination in plants. PLANT CELL REPORTS 2003; 21:1135-1142. [PMID: 12910366 DOI: 10.1007/s00299-003-0644-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2003] [Revised: 04/16/2003] [Accepted: 04/16/2003] [Indexed: 05/24/2023]
Abstract
Attempts for establishing an efficient gene targeting (GT) system in seed plants have hitherto not been successful. In contrast, GT based on homologous recombination is highly efficient in Physcomitrella, making this moss a novel tool in reverse genetics. However, why homologous and illegitimate recombination are differently regulated between Physcomitrella and seed plants is still enigmatic. Here we update the state of the art of GT in Physcomitrella and discuss approaches to unravel this enigma. Identification of molecular factors significantly enhancing GT and their subsequent transfer to crop plants will have a great impact on plant biotechnology by enabling precise genetic engineering. Physcomitrella appears to be the most useful model system in this context.
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Affiliation(s)
- A Hohe
- Plant Biotechnology, Freiburg University, Schaenzlestrasse 1, 79104, Freiburg, Germany
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Puchta H. Towards the ideal GMP: homologous recombination and marker gene excision. JOURNAL OF PLANT PHYSIOLOGY 2003; 160:743-754. [PMID: 12940543 DOI: 10.1078/0176-1617-01027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A mayor aim of biotechnology is the establishment of techniques for the precise manipulation of plant genomes. Two major efforts have been undertaken over the last dozen years, one to set up techniques for site-specific alteration of the plant genome via homologous recombination ("gene targeting") and the other for the removal of selectable marker genes from transgenic plants. Unfortunately, despite multiple promising approaches that will be shortly described in this review no feasible gene targeting technique has been developed till now for crop plants. In contrast, several alternative procedures have been established successfully to remove selectable markers from plant genomes. Intriguingly besides techniques relying on transposons and site-specific recombinases, recent results indicate that homologous recombination might be a valuable alternative for the excision of marker genes.
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Affiliation(s)
- Holger Puchta
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany.
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50
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Orel N, Puchta H. Differences in the processing of DNA ends in Arabidopsis thaliana and tobacco: possible implications for genome evolution. PLANT MOLECULAR BIOLOGY 2003; 51:523-31. [PMID: 12650618 DOI: 10.1023/a:1022324205661] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Surprising species-specific differences in non-homologous end-joining (NHEJ) of genomic double-strand breaks (DSBs) have been reported for the two dicotyledonous plants Arabidopsis thaliana and Nicotiana tabacum. In Arabidopsis deletions were, on average, larger than in tobacco and not associated with insertions. To establish the molecular basis of the phenomenon we analysed the fate of free DNA ends in both plant species by biolistic transformation of leaf tissue with linearized plasmid molecules. Southern blotting indicated that, irrespective of the nature of the ends (blunt, 5' or 3' overhangs), linearized full-length DNA molecules were, on average, more stable in tobacco than in Arabidopsis. The relative expression of a beta-glucuronidase gene encoded by the plasmid was similar in both plant species when the break was distant from the marker gene. However, if a DSB was introduced between the promoter and the open reading frame of the marker, transient expression was halved in Arabidopsis as compared to tobacco. These results indicate that free DNA ends are more stable in tobacco than in Arabidopsis, either due to lower DNA exonuclease activity or due to a better protection of DNA break ends or both. Exonucleolytic degradation of DNA ends might be a driving force in the evolution of genome size as the Arabidopsis genome is more than twenty times smaller than the tobacco genome.
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Affiliation(s)
- Nadiya Orel
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, 06466 Gatersleben, Germany
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