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Ren B, Liu L, Li S, Kuang Y, Wang J, Zhang D, Zhou X, Lin H, Zhou H. Cas9-NG Greatly Expands the Targeting Scope of the Genome-Editing Toolkit by Recognizing NG and Other Atypical PAMs in Rice. MOLECULAR PLANT 2019; 12:1015-1026. [PMID: 30928635 DOI: 10.1016/j.molp.2019.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 05/13/2023]
Abstract
CRISPR technologies enabling precise genome manipulation are valuable for gene function studies and molecular crop breeding. However, the requirement of a protospacer adjacent motif (PAM), such as NGG and TTN, for Cas protein recognition restricts the selection of targetable genomic loci in practical applications of CRISPR technologies. Recently Cas9-NG, which recognizes a minimal NG PAM, was reported to expand the targeting space of genome editing in human cells, but it remains unclear whether this Cas9 variant can be used in plants. In this study, we evaluated the nuclease activity of Cas9-NG toward various NGN PAMs by targeting endogenous genes in transgenic rice. We found that Cas9-NG edits all NGG, NGA, NGT, and NGC sites with impaired activity, while the gene-edited plants were dominated by monoallelic mutations. Cas9-NG-engineered base editors were then developed and used to generate OsBZR1 gain-of-function plants that can not be created by other available Cas9-engineered base editors. Moreover, we showed that a Cas9-NG-based transcriptional activator efficiently upregulated the expression of endogenous target genes in rice. In addition, we discovered that Cas9-NG recognizes NAC, NTG, NTT, and NCG apart from NG PAM. Together, these findings demonstrate that Cas9-NG can greatly expand the targeting scope of genome-editing tools, showing great potential for targeted genome editing, base editing, and genome regulation in plants.
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Affiliation(s)
- Bin Ren
- Ministry of Education Key Laboratory of Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610065, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shaofang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongjie Kuang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingwen Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dawei Zhang
- Ministry of Education Key Laboratory of Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Honghui Lin
- Ministry of Education Key Laboratory of Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Schiermeyer A, Schneider K, Kirchhoff J, Schmelter T, Koch N, Jiang K, Herwartz D, Blue R, Marri P, Samuel P, Corbin DR, Webb SR, Gonzalez DO, Folkerts O, Fischer R, Schinkel H, Ainley WM, Schillberg S. Targeted insertion of large DNA sequences by homology-directed repair or non-homologous end joining in engineered tobacco BY-2 cells using designed zinc finger nucleases. PLANT DIRECT 2019; 3:e00153. [PMID: 31360827 PMCID: PMC6639735 DOI: 10.1002/pld3.153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/11/2019] [Accepted: 07/03/2019] [Indexed: 05/13/2023]
Abstract
Targeted integration of recombinant DNA fragments into plant genomes by DNA double-strand break (DSB) repair mechanisms has become a powerful tool for precision engineering of crops. However, many targeting platforms require the screening of many transgenic events to identify a low number of targeted events among many more random insertion events. We developed an engineered transgene integration platform (ETIP) that uses incomplete marker genes at the insertion site to enable rapid phenotypic screening and recovery of targeted events upon functional reconstitution of the marker genes. The two marker genes, encoding neomycin phosphotransferase II (nptII) and Discosoma sp. red fluorescent protein (DsRed) enable event selection on kanamycin-containing selective medium and subsequent screening for red fluorescent clones. The ETIP design allows targeted integration of donor DNA molecules either by homology-directed repair (HDR) or non-homologous end joining (NHEJ)-mediated mechanisms. Targeted donor DNA integration is facilitated by zinc finger nucleases (ZFN). The ETIP cassette was introduced into Nicotiana tabacum BY-2 suspension cells to generate target cell lines containing a single copy locus of the transgene construct. The utility of the ETIP platform has been demonstrated by targeting DNA constructs containing up to 25-kb payload. The success rate for clean targeted DNA integration was up to 21% for HDR and up to 41% for NHEJ based on the total number of calli analyzed by next-generation sequencing (NGS). The rapid generation of targeted events with large DNA constructs expands the utility of the nuclease-mediated gene addition platform both for academia and the commercial sector.
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Affiliation(s)
- Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Katja Schneider
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Janina Kirchhoff
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Thomas Schmelter
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Natalie Koch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Ke Jiang
- Corteva AgriscienceIndianapolisINUSA
| | - Denise Herwartz
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Ryan Blue
- Corteva AgriscienceIndianapolisINUSA
| | | | | | | | | | | | | | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Indiana Biosciences Research InstituteIndianapolisINUSA
| | - Helga Schinkel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | | | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
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An insight into the folding and stability of Arabidopsis thaliana SOG1 transcription factor under salinity stress in vitro. Biochem Biophys Res Commun 2019; 515:531-537. [PMID: 31176488 DOI: 10.1016/j.bbrc.2019.05.183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 11/20/2022]
Abstract
The present study describes the biophysical characterization of Arabidopsis thaliana SOG1 (SUPPRESSOR OF GAMMA RESPONSE 1) protein, a NAC domain transcription factor which plays central role in DNA damage response pathway, under salinity stress in vitro. Tryptophan fluorescence studies using purified recombinant wild type (full length) AtSOG1 and its N-terminal or C-terminal deletion forms (AtSOG1ΔNAC and AtSOG1ΔCT respectively) have revealed high salinity induced conformational change due to removal of the N-terminal NAC domain. Bis-ANS binding assays indicate that removal of the N-terminal NAC domain increases the surface hydrophobic binding sites, while the C-terminal region of SOG1 also plays important role in regulating the surface hydrophobicity aspects following exposure to high salinity. Circular dichroism (CD) spectral studies have indicated that removal of the N-terminal NAC domain affects the structural conformation of the protein under high salt concentration. Urea-induced equilibrium unfolding studies revealed decreased stability of C-terminal region due to removal of the N-terminal NAC domain. In vitro aggregation studies have indicated higher propensity of aggregation of AtSOG1ΔNAC due to salt treatment. Overall, our results provide evidence for the importance of both N-terminal NAC domain and the C-terminal region in regulating the stability of SOG1 protein under salinity stress in vitro.
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Guyon-Debast A, Rossetti P, Charlot F, Epert A, Neuhaus JM, Schaefer DG, Nogué F. The XPF-ERCC1 Complex Is Essential for Genome Stability and Is Involved in the Mechanism of Gene Targeting in Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2019; 10:588. [PMID: 31143199 PMCID: PMC6521618 DOI: 10.3389/fpls.2019.00588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
The XPF-ERCC1 complex, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair, and homologous recombination. XPF-ERCC1 incises double-stranded DNA at double-strand/single-strand junctions, making it an ideal enzyme for processing DNA structures that contain partially unwound strands. Here, we have examined the role of the XPF-ERCC1 complex in the model bryophyte Physcomitrella patens which exhibits uniquely high gene targeting frequencies. We undertook targeted knockout of the Physcomitrella ERCC1 and XPF genes. Mutant analysis shows that the endonuclease complex is essential for resistance to UV-B and to the alkylating agent MMS, and contributes to the maintenance of genome integrity but is also involved in gene targeting in this model plant. Using different constructs we determine whether the function of the XPF-ERCC1 endonuclease complex in gene targeting was removal of 3' non-homologous termini, similar to SSA, or processing of looped-out heteroduplex intermediates. Interestingly, our data suggest a role of the endonuclease in both pathways and have implications for the mechanism of targeted gene replacement in plants and its specificities compared to yeast and mammalian cells.
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Affiliation(s)
- Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Patricia Rossetti
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Aline Epert
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Jean-Marc Neuhaus
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Didier G. Schaefer
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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55
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Mahapatra K, De S, Banerjee S, Roy S. Pesticide mediated oxidative stress induces genotoxicity and disrupts chromatin structure in fenugreek (Trigonella foenum - graecum L.) seedlings. JOURNAL OF HAZARDOUS MATERIALS 2019; 369:362-374. [PMID: 30784966 DOI: 10.1016/j.jhazmat.2019.02.056] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Here we report cytototoxic and genotoxic potentials of four commonly used pesticides, including, tricyclazole, thiabendazole (fungicides), plethora and slash-360 (insecticides) in the non-target tropical crop plant Trigonella foenum - graecum L. (fenugreek). Three different concentrations of the selected pesticides were used. For fungicides, 0.05% and for insecticides, 0.1% concentration represents recommended doses, while, 2X and 4X concentrations of the recommended dose were used to test their phytotoxic effects. Inhibition of germination and seedling growth were clearly observed at 4X concentration of the pesticides. Tricyclazole and plethora showed more pronounced effects than the other two agrochemicals. The pesticides, particularly at 4X concentrations clearly induced oxidative stress and cytotoxic effects in Trigonella seedlings with appreciable reduction in mitotic index, induction of chromosomal abnormalities in root meristematic cell and decreased level of accumulation of some key cell cycle regulators, including CDK1, CDK2 and Cyclin B1.Detection of accumulation of DNA double strand breaks and histone H2AX phosphorylation in pesticide treated seedlings have revealed direct genotoxic effects of the selected pesticides. Overall, our results provide insights into the mechanism of pesticide induced cytotoxic and genotoxic effects in plant genome with future implications for designing pesticides to minimize their deleterious effects on non-target crop plants.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India
| | - Sayanti De
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India
| | - Samrat Banerjee
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India.
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Nandy S, Pathak B, Zhao S, Srivastava V. Heat-shock-inducible CRISPR/Cas9 system generates heritable mutations in rice. PLANT DIRECT 2019; 3:e00145. [PMID: 31404128 PMCID: PMC6603394 DOI: 10.1002/pld3.145] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 05/22/2023]
Abstract
Transient expression of CRISPR/Cas9 is an effective approach for limiting its activities and improving its precision in genome editing. Here, we describe the heat-shock-inducible CRISPR/Cas9 for controlled genome editing, and demonstrate its efficiency in the model crop, rice. Using the soybean heat-shock protein gene promoter and the rice U3 promoter to express Cas9 and sgRNA, respectively, we developed the heat-shock (HS)-inducible CRISPR/Cas9 system, and tested its efficacy in targeted mutagenesis. Two loci were targeted in rice, and the presence of targeted mutations was determined before and after the HS treatment. Only a low rate of targeted mutagenesis was detected before HS (~16%), but an increased rate of mutagenesis was observed after the HS treatment among the transgenic lines (50-63%). Analysis of regenerated plants harboring HS-CRISPR/Cas9 revealed that targeted mutagenesis was suppressed in the plants but induced by HS, which was detectable by Sanger sequencing after a few weeks of HS treatments. Most importantly, the HS-induced mutations were transmitted to the progeny at a high rate, generating monoallelic and biallelic mutations that independently segregated from the Cas9 gene. Additionally, off-target mutations were either undetectable or found at a lower rate in HS-CRISPR/Cas9 lines as compared to the constitutive-overexpression CRISPR/Cas9 lines. Taken together, this work shows that HS-CRISPR/Cas9 is a controlled and reasonably efficient platform for genome editing, and therefore, a promising tool for limiting genome-wide off-target effects and improving the precision of genome editing.
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Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
| | - Bhuvan Pathak
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas
| | - Shan Zhao
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas
- Department of Horticulture University of Arkansas Fayetteville Arkansas
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57
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Gang H, Liu G, Zhang M, Zhao Y, Jiang J, Chen S. Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant. BMC Genomics 2019; 20:311. [PMID: 31014254 PMCID: PMC6480916 DOI: 10.1186/s12864-019-5636-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/24/2019] [Indexed: 11/29/2022] Open
Abstract
Background Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research. T-DNA integration in plants is complex and still largely unknown. In this work, we reported that multiple T-DNA fragments caused chromosomal translocation and deletion in a birch (Betula platyphylla × B. pendula) T-DNA mutant yl. Results We performed PacBio genome resequencing for yl and the result revealed that two ends of a T-DNA can be integrated into plant genome independently because the two ends can be linked to different chromosomes and cause chromosomal translocation. We also found that these T-DNA were connected into tandem fragment regardless of direction before integrating into plant genome. In addition, the integration of T-DNA in yl genome also caused several chromosomal fragments deletion. We then summarized three cases for T-DNA integration model in the yl genome. (1) A T-DNA fragment is linked to the two ends of a double-stranded break (DSB); (2) Only one end of a T-DNA fragment is linked to a DSB; (3) A T-DNA fragment is linked to the ends of different DSBs. All the observations in the yl genome supported the DSB repair model. Conclusions In this study, we showed a comprehensive genome analysis of a T-DNA mutant and provide a new insight into T-DNA integration in plants. These findings would be helpful for the analysis of T-DNA mutants with special phenotypes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5636-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huixin Gang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Manman Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yuming Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Dual-targeting by CRISPR/Cas9 leads to efficient point mutagenesis but only rare targeted deletions in the rice genome. 3 Biotech 2019; 9:158. [PMID: 30944805 PMCID: PMC6439133 DOI: 10.1007/s13205-019-1690-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/20/2019] [Indexed: 11/05/2022] Open
Abstract
The present study investigated the efficiency of CRISPR/Cas9 in creating genomic deletions as the basis of its application in removing selection marker genes or the intergenic regions. Three loci, representing a transgene and two rice genes, were targeted at two sites each, in separate experiments, and the deletion of the defined fragments was investigated by PCR and sequencing. Genomic deletions were found at a low rate among the transformed callus lines that could be isolated, cultured, and regenerated into plants harboring the deletion. However, randomly regenerated plants showed mixed genomic effects, and generally did not harbor heritable genomic deletions. To determine whether point mutations occurred at each targeted site, a total of 114 plants consisting of primary transgenic lines and their progeny were analyzed. Ninety-three plants showed targeting, 60 of which were targeted at both sites. The presence of point mutations at both sites was correlated with the guide RNA efficiency. In summary, genomic deletions through dual-targeting by the paired-guide RNAs were generally observed in callus, while de novo point mutations at one or both sites occurred at high rates in transgenic plants and their progeny, generating a variety of insertion–deletions or single-nucleotide variations. In this study, point mutations were exceedingly favored over genomic deletions; therefore, for the recovery of plant lines harboring targeted deletions, identifying early transformed clones harboring the deletions, and isolating them for plant regeneration is recommended.
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Zedek F, Bureš P. Pest Arthropods with Holocentric Chromosomes are More Resistant to Sterilizing Ionizing Radiation. Radiat Res 2019; 191:255-261. [PMID: 30702973 DOI: 10.1667/rr15208.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
It has been hypothesized that species with holocentric chromosomes have a selective evolutionary advantage for developmental and reproductive success because holocentric chromosomes are less susceptible to chromosome breakage than monocentric chromosomes. We analyzed data on sterilizing doses of ionizing radiation for more than 250 species of arthropods to test whether the minimal dose for reproductive sterilization is higher for species with holocentric chromosomes than for species with monocentric chromosomes. Using linear mixed models that account for phylogeny, we show that holocentric arthropods are more tolerant of sterilizing radiation than monocentrics. Moreover, higher dose rates correlate with lower sterilizing doses in monocentrics, but not in holocentrics, which is a novel finding that may be of importance for radiosanitation practice. Under the dose rate of 1 Gy/min, holocentric arthropods are sterilized on average with a 2.9 times higher minimal dose than monocentrics. Life stage and sex have significant but considerably weaker effects on sterilizing dose than chromosome type. Adults and males require 1.2 and 1.4 times higher sterilizing doses than juveniles and females, respectively. These results support the hypothesis that holocentric lineages may originate and thrive better in times of increased exposure to chromosome-breaking factors.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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Hirakawa T, Matsunaga S. Characterization of DNA Repair Foci in Root Cells of Arabidopsis in Response to DNA Damage. FRONTIERS IN PLANT SCIENCE 2019; 10:990. [PMID: 31417598 PMCID: PMC6682680 DOI: 10.3389/fpls.2019.00990] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/15/2019] [Indexed: 05/20/2023]
Abstract
As a sessile organism, plants are constantly challenged by diverse environmental stresses that threaten genome integrity by way of induction of DNA damage. In plants, each tissue is composed of differentiated cell types, and the response to DNA damage differs among each cell type. However, limited information is available on the subnuclear dynamics of different cell types in response to DNA damage in plants. A chromatin remodeling factor RAD54, which plays an important role in the exchange reaction and alteration of chromatin structure during homologous recombination, specifically accumulates at damaged sites, forming DNA repair foci (termed RAD54 foci) in nuclei after γ-irradiation. In this study, we performed a time-course analysis of the appearance of RAD54 foci in root cells of Arabidopsis after γ-irradiation to characterize the subnuclear dynamics in each cell type. A short time after γ-irradiation, no significant difference in detection frequency of RAD54 foci was observed among epidermal, cortical, and endodermal cells in the meristematic zone of roots. Interestingly, cells showing RAD54 foci persisted in roots at long time after γ-irradiation, and RAD54 foci in these cells localized to nuclear periphery with high frequency. These observations suggest that the nuclear envelope plays a role in the maintenance of genome stability in response to DNA damage in Arabidopsis roots.
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61
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A Highly Efficient Cell Division-Specific CRISPR/Cas9 System Generates Homozygous Mutants for Multiple Genes in Arabidopsis. Int J Mol Sci 2018; 19:ijms19123925. [PMID: 30544514 PMCID: PMC6321140 DOI: 10.3390/ijms19123925] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/02/2022] Open
Abstract
The CRISPR/Cas9 system has been widely used for targeted genome editing in numerous plant species. In Arabidopsis, constitutive promoters usually result in a low efficiency of heritable mutation in the T1 generation. In this work, CRISPR/Cas9 gene editing efficiencies using different promoters to drive Cas9 expression were evaluated. Expression of Cas9 under the constitutive CaMV 35S promoter resulted in a 2.3% mutation rate in T1 plants and failed to produce homozygous mutations in the T1 and T2 generations. In contrast, expression of Cas9 under two cell division-specific promoters, YAO and CDC45, produced mutation rates of 80.9% to 100% in the T1 generation with nonchimeric mutations in the T1 (4.4–10%) and T2 (32.5–46.1%) generations. The pCDC45 promoter was used to modify a previously reported multiplex CRISPR/Cas9 system, replacing the original constitutive ubiquitin promoter. The multi-pCDC45-Cas9 system produced higher mutation efficiencies than the multi-pUBQ-Cas9 system in the T1 generation (60.17% vs. 43.71%) as well as higher efficiency of heritable mutations (11.30% vs. 4.31%). Sextuple T2 homozygous mutants were identified from a construct targeting seven individual loci. Our results demonstrate the advantage of using cell division promoters for CRISPR/Cas9 gene editing applications in Arabidopsis, especially in multiplex applications.
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Han TT, Liu WC, Lu YT. General control non-repressible 20 (GCN20) functions in root growth by modulating DNA damage repair in Arabidopsis. BMC PLANT BIOLOGY 2018; 18:274. [PMID: 30419826 PMCID: PMC6233562 DOI: 10.1186/s12870-018-1444-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 09/27/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Most ABC transporters are engaged in transport of various compounds, but its subfamily F lacks transmembrane domain essential for chemical transportation. Thus the function of subfamily F remains further elusive. RESULTS Here, we identified General Control Non-Repressible 20 (GCN20), a member of subfamily F, as new factor for DNA damage repair in root growth. While gcn20-1 mutant had a short primary root with reduced meristem size and cell number, similar primary root lengths were assayed in both wild-type and GCN20::GCN20 gcn20-1 plants, indicating the involvement of GCN20 in root elongation. Further experiments with EdU incorporation and comet assay demonstrated that gcn20-1 displays increased cell cycle arrest at G2/M checkpoint and accumulates more damaged DNA. This is possible due to impaired ability of DNA repair in gcn20-1 since gcn20-1 seedlings are hypersensitive to DNA damage inducers MMC and MMS compared with the wild type plants. This note was further supported by the observation that gcn20-1 is more sensitive than the wild type when subjected to UV treatment in term of changes of both fresh weight and survival rate. CONCLUSIONS Our study indicates that GCN20 functions in primary root growth by modulating DNA damage repair in Arabidopsis. Our study will be useful to understand the functions of non-transporter ABC proteins in plant growth.
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Affiliation(s)
- Tong-Tong Han
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Wen-Cheng Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
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Wozny D, Kramer K, Finkemeier I, Acosta IF, Koornneef M. Genes for seed longevity in barley identified by genomic analysis on near isogenic lines. PLANT, CELL & ENVIRONMENT 2018; 41:1895-1911. [PMID: 29744896 DOI: 10.1111/pce.13330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 05/15/2023]
Abstract
Genes controlling differences in seed longevity between 2 barley (Hordeum vulgare) accessions were identified by combining quantitative genetics "omics" technologies in near isogenic lines (NILs). The NILs were derived from crosses between the spring barley landraces L94 from Ethiopia and Cebada Capa from Argentina. A combined transcriptome and proteome analysis on mature, nonaged seeds of the 2 parental lines and the L94 NILs by RNA-sequencing and total seed proteomic profiling identified the UDP-glycosyltransferase MLOC_11661.1 as candidate gene for the quantitative trait loci on 2H, and the NADP-dependent malic enzyme (NADP-ME) MLOC_35785.1 as possible downstream target gene. To validate these candidates, they were expressed in Arabidopsis under the control of constitutive promoters to attempt complementing the T-DNA knockout line nadp-me1. Both the NADP-ME MLOC_35785.1 and the UDP-glycosyltransferase MLOC_11661.1 were able to rescue the nadp-me1 seed longevity phenotype. In the case of the UDP-glycosyltransferase, with high accumulation in NILs, only the coding sequence of Cebada Capa had a rescue effect.
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Affiliation(s)
- Dorothee Wozny
- Institute Jean-Pierre Bourgin INRA Centre de Versailles-Grignon, Route de Saint-Cyr 10, Versailles Cedex, 78026, France
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
| | - Katharina Kramer
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
| | - Iris Finkemeier
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Ivan F Acosta
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
| | - Maarten Koornneef
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
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Litvinov S, Rashydov N. Transgenerational Transmission of Radiation-Induced Expression Patterns of Arabidopsis Thaliana (L.) Heynh. Rad51 and Rad1 Genes. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2018. [DOI: 10.21448/ijsm.415191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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65
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Chen P, Li R, Zhou R. Comparative phosphoproteomic analysis reveals differentially phosphorylated proteins regulate anther and pollen development in kenaf cytoplasmic male sterility line. Amino Acids 2018; 50:841-862. [DOI: 10.1007/s00726-018-2564-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/29/2018] [Indexed: 12/28/2022]
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Zedek F, Bureš P. Holocentric chromosomes: from tolerance to fragmentation to colonization of the land. ANNALS OF BOTANY 2018; 121:9-16. [PMID: 29069342 PMCID: PMC5786251 DOI: 10.1093/aob/mcx118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/24/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The dispersed occurrence of holocentric chromosomes across eukaryotes implies they are adaptive, but the conditions under which they confer an advantage over monocentric chromosomes remain unclear. Due to their extended kinetochore and the attachment of spindle microtubules along their entire length, holocentric chromosomes tolerate fragmentation; hence, they may be advantageous in times of exposure to factors that cause chromosomal fragmentation (clastogens). SCOPE It is shown that holocentric organisms may, indeed, thrive better than monocentric organisms under clastogenic conditions and that such conditions of various duration and intensity have occurred many times throughout the history of Earth's biota. One of the most important clastogenic events in eukaryotic history, in which holocentric chromosomes may have played the key role, was the colonization of land by plants and animals half a billion years ago. In addition to arguments supporting the anticlastogenic hypothesis of holocentric chromosomes and a discussion of its evolutionary consequences, experiments and analyses are proposed to explore this hypothesis in more depth. CONCLUSIONS It is argued that the tolerance to clastogens explains the origin of holocentric lineages and may also have far-reaching consequences for eukaryotic evolution in general as exemplified by the potential role of holocentric chromosomes in terrestrialization.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlarska, Brno, Czech Republic
- For correspondence. E-mail
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlarska, Brno, Czech Republic
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Katarzyna Banas A, Hermanowicz P, Sztatelman O, Labuz J, Aggarwal C, Zglobicki P, Jagiello-Flasinska D, Strzalka W. 6,4-PP Photolyase Encoded by AtUVR3 is Localized in Nuclei, Chloroplasts and Mitochondria and its Expression is Down-Regulated by Light in a Photosynthesis-Dependent Manner. PLANT & CELL PHYSIOLOGY 2018; 59:44-57. [PMID: 29069446 DOI: 10.1093/pcp/pcx159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 10/19/2017] [Indexed: 05/04/2023]
Abstract
Pyrimidine dimers are the most important DNA lesions induced by UVB irradiation. They can be repaired directly by photoreactivation or indirectly by the excision repair pathways. Photoreactivation is carried out by photolyases, enzymes which bind to the dimers and use the energy of blue light or UVA to split bonds between adjacent pyrimidines. Arabidopsis thaliana has three known photolyases: AtPHR1, AtCRY3 and AtUVR3. Little is known about the cellular localization and regulation of AtUVR3 expression. We have found that its transcript level is down-regulated by light (red, blue or white) in a photosynthesis-dependent manner. The down-regulatory effect of red light is absent in mature leaves of the phyB mutant, but present in leaves of phyAphyB. UVB irradiation does not increase AtUVR3 expression in leaves. Transiently expressed AtUVR3-green fluorescent protein (GFP) is found in the nuclei, chloroplasts and mitochondria of Nicotiana benthamiana epidermal cells. In the nucleoplasm, AtUVR3-GFP is distributed uniformly, while in the nucleolus it forms speckles. Truncated AtUVR3 and muteins were used to identify the sequences responsible for its subcellular localization. Mitochondrial and chloroplast localization of AtUVR3 is independent of its N-terminal sequence. Amino acids located at the C-terminal loop of the protein are involved in its transport into chloroplasts and its retention inside the nucleolus.
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Affiliation(s)
- Agnieszka Katarzyna Banas
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
- The Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Pawel Hermanowicz
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
- The Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Olga Sztatelman
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland
| | - Justyna Labuz
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
- The Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Chhavi Aggarwal
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
- Department of Gene Expression, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Piotr Zglobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Dominika Jagiello-Flasinska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
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Risk associated with off-target plant genome editing and methods for its limitation. Emerg Top Life Sci 2017; 1:231-240. [PMID: 33525760 PMCID: PMC7288994 DOI: 10.1042/etls20170037] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/13/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022]
Abstract
Assessment for potential adverse effects of plant genome editing logically focuses on the specific characteristics of the derived phenotype and its release environment. Genome-edited crops, depending on the editing objective, can be classified as either indistinguishable from crops developed through conventional plant breeding or as crops which are transgenic. Therefore, existing regulatory regimes and risk assessment procedures accommodate genome-edited crops. The ability for regulators and the public to accept a product focus in the evaluation of genome-edited crops will depend on research which clarifies the precision of the genome-editing process and evaluates unanticipated off-target edits from the process. Interpretation of genome-wide effects of genome editing should adhere to existing frameworks for comparative risk assessment where the nature and degree of effects are considered relative to a baseline of genome-wide mutations as found in crop varieties developed through conventional breeding methods. Research addressing current uncertainties regarding unintended changes from plant genome editing, and adopting procedures that clearly avoid the potential for gene drive initiation, will help to clarify anticipated public and regulatory questions regarding risk of crops derived through genome editing.
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69
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Velappan Y, Signorelli S, Considine MJ. Cell cycle arrest in plants: what distinguishes quiescence, dormancy and differentiated G1? ANNALS OF BOTANY 2017; 120:495-509. [PMID: 28981580 PMCID: PMC5737280 DOI: 10.1093/aob/mcx082] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/29/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Quiescence is a fundamental feature of plant life, which enables plasticity, renewal and fidelity of the somatic cell line. Cellular quiescence is defined by arrest in a particular phase of the cell cycle, typically G1 or G2; however, the regulation of quiescence and proliferation can also be considered across wider scales in space and time. As such, quiescence is a defining feature of plant development and phenology, from meristematic stem cell progenitors to terminally differentiated cells, as well as dormant or suppressed seeds and buds. While the physiology of each of these states differs considerably, each is referred to as 'cell cycle arrest' or 'G1 arrest'. SCOPE Here the physiology and molecular regulation of (1) meristematic quiescence, (2) dormancy and (3) terminal differentiation (cell cycle exit) are considered in order to determine whether and how the molecular decisions guiding these nuclear states are distinct. A brief overview of the canonical cell cycle regulators is provided, and the genetic and genomic, as well as physiological, evidence is considered regarding two primary questions: (1) Are the canonical cell cycle regulators superior or subordinate in the regulation of quiescence? (2) Are these three modes of quiescence governed by distinct molecular controls? CONCLUSION Meristematic quiescence, dormancy and terminal differentiation are each predominantly characterized by G1 arrest but regulated distinctly, at a level largely superior to the canonical cell cycle. Meristematic quiescence is intrinsically linked to non-cell-autonomous regulation of meristem cell identity, and particularly through the influence of ubiquitin-dependent proteolysis, in partnership with reactive oxygen species, abscisic acid and auxin. The regulation of terminal differentiation shares analogous features with meristematic quiescence, albeit with specific activators and a greater role for cytokinin signalling. Dormancy meanwhile appears to be regulated at the level of chromatin accessibility, by Polycomb group-type histone modifications of particular dormancy genes.
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Affiliation(s)
- Yazhini Velappan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- The School of Molecular Sciences, and The UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Santiago Signorelli
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- The School of Molecular Sciences, and The UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Departamento de Biología Vegetal, Universidad de la República, Montevideo, 12900, Uruguay
| | - Michael J Considine
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- The School of Molecular Sciences, and The UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Department of Agriculture and Food Western Australia, South Perth, WA 6151, Australia
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
- For correspondence. Email
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71
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Vu GTH, Cao HX, Reiss B, Schubert I. Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage. THE NEW PHYTOLOGIST 2017; 214:1712-1721. [PMID: 28245065 DOI: 10.1111/nph.14490] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/22/2017] [Indexed: 06/06/2023]
Abstract
In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate. We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution. Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome. Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Bernd Reiss
- Max Planck Institute for Plant Breeding Research, 50829, Köln, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
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72
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Horvath BM, Kourova H, Nagy S, Nemeth E, Magyar Z, Papdi C, Ahmad Z, Sanchez-Perez GF, Perilli S, Blilou I, Pettkó-Szandtner A, Darula Z, Meszaros T, Binarova P, Bogre L, Scheres B. Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control. EMBO J 2017; 36:1261-1278. [PMID: 28320736 PMCID: PMC5412863 DOI: 10.15252/embj.201694561] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 12/26/2022] Open
Abstract
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These γH2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta Genetic interaction between the RBR-silenced amiRBR and Atbrca1 mutants suggests that RBR and AtBRCA1 may function together in maintaining genome integrity. Together with E2FA, RBR is directly involved in the transcriptional DNA damage response as well as in the cell death pathway that is independent of SOG1, the plant functional analogue of p53. Thus, plant homologs and analogues of major mammalian tumour suppressor proteins form a regulatory network that coordinates cell proliferation with cell and genome integrity.
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Affiliation(s)
- Beatrix M Horvath
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Hana Kourova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Szilvia Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Edit Nemeth
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zoltan Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Papdi
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zaki Ahmad
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Gabino F Sanchez-Perez
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Serena Perilli
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Ikram Blilou
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | | | - Zsuzsanna Darula
- Laboratory of Proteomic Research, Biological Research Centre, Szeged, Hungary
| | - Tamas Meszaros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
- Technical Analytical Research Group of HAS, Budapest, Hungary
| | - Pavla Binarova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Laszlo Bogre
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Ben Scheres
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
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Davies JP, Kumar S, Sastry-Dent L. Use of Zinc-Finger Nucleases for Crop Improvement. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:47-63. [PMID: 28712500 DOI: 10.1016/bs.pmbts.2017.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the past two decades, new technologies enabling targeted modification of plant genomes have been developed. Among these are zinc-finger nucleases (ZFNs) which are composed of engineered zinc-finger DNA-binding domains fused with a nuclease, generally the FokI nuclease. The zinc-finger domains are composed of a series of four to six 30 amino acid domains that can bind to trinucleotide sequences giving the entire DNA-binding domain specificity to 12-18 nucleotides. Since the FokI nuclease functions as a dimer, pairs of zinc-finger domains are designed to bind upstream and downstream of the cut site which increases the specificity of the complete ZFN to 24-36 nucleotides. The ability of these engineered nucleases to create targeted double-stranded breaks at designated locations throughout the genome has enabled precise deletion, addition, and editing of genes. These techniques are being used to create new genetic variation by deleting or editing endogenous gene sequences and enhancing the efficiency of transgenic product development through targeted insertion of transgenes to specific genomic locations and to sequentially add and/or delete transgenes from existing transgenic events.
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Hirakawa T, Hasegawa J, White CI, Matsunaga S. RAD54 forms DNA repair foci in response to DNA damage in living plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:372-382. [PMID: 28155243 DOI: 10.1111/tpj.13499] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
Plants have various defense mechanisms against environmental stresses that induce DNA damage. Genetic and biochemical analyses have revealed the sensing and signaling of DNA damage, but little is known about subnuclear dynamics in response to DNA damage in living plant cells. Here, we observed that the chromatin remodeling factor RAD54, which is involved in DNA repair via the homologous recombination pathway, formed subnuclear foci (termed RAD54 foci) in Arabidopsis thaliana after induction of DNA double-strand breaks. The appearance of RAD54 foci was dependent on the ATAXIA-TELANGIECTASIA MUTATED-SUPPRESSOR OF GAMMA RESPONSE 1 pathway, and RAD54 foci were co-localized with γH2AX signals. Laser irradiation of a subnuclear area demonstrated that in living cells RAD54 was specifically accumulated at the damaged site. In addition, the formation of RAD54 foci showed specificity for cell type and region. We conclude that RAD54 foci correspond to DNA repair foci in A. thaliana.
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Affiliation(s)
- Takeshi Hirakawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Junko Hasegawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Université Blaise Pascal, Clermont-Ferrand, France
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
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Macovei A, Sahoo RK, Faè M, Balestrazzi A, Carbonera D, Tuteja N. Overexpression of PDH45 or SUV3 helicases in rice leads to delayed leaf senescence-associated events. PROTOPLASMA 2017; 254:1103-1113. [PMID: 27586643 DOI: 10.1007/s00709-016-1017-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
Senescence is a very complex process characterized by a highly regulated series of degenerative events which include changes in cell structure, metabolism and gene expression. In animals, one of the indicators of senescence is telomere shortening. In plants, this aspect is more puzzling because telomere shortening is not always correlated with senescence. In some cases, there were no differences in telomere length during plant developmental stages while in other cases both shortening and lengthening have been observed. Several genes involved in telomere homeostasis have been identified in plants, including some helicases. In the present study, the salinity stress-tolerant transgenic IR64 rice plants overexpressing the PDH45 (Pea DNA Helicase 45) or SUV3 (Suppressor of Var1-3) genes were used to test their performance during natural senescence at flowering (S2) and seed maturation (S4) developmental stages. Our results reveal that both PDH45 and SUV3 transgenic rice lines present decreased levels of necrosis/apoptosis as compared to wild type plants. Additionally, in these plants, some senescence-associated genes (SAGs) were downregulated at S2 and S4 stages, while genes involved in the maintenance of genome stability and DNA repair were upregulated. More interestingly, the telomeres were up to 3.8-fold longer in the SUV3 overexpressing lines as compared to wild type plants. This was associated with an increase (2.5-fold) in telomerase (OsTERT) transcript level. This is an interesting result reporting a possible involvement of SUV3 in telomere homeostasis in plants.
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Affiliation(s)
- Anca Macovei
- Plant Molecular Biology Group, International Center for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110067, New Delhi, India
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Ranjan K Sahoo
- Plant Molecular Biology Group, International Center for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110067, New Delhi, India
| | - Matteo Faè
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Daniela Carbonera
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Center for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110067, New Delhi, India.
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, E2-Block, Sector 125, Noida, UP, 201313, India.
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Schedel S, Pencs S, Hensel G, Müller A, Rutten T, Kumlehn J. RNA-Guided Cas9-Induced Mutagenesis in Tobacco Followed by Efficient Genetic Fixation in Doubled Haploid Plants. FRONTIERS IN PLANT SCIENCE 2017; 7:1995. [PMID: 28101094 PMCID: PMC5209389 DOI: 10.3389/fpls.2016.01995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/16/2016] [Indexed: 05/08/2023]
Abstract
Customizable endonucleases are providing an effective tool for genome engineering. The resulting primary transgenic individuals (T0) are typically heterozygous and/or chimeric with respect to any mutations induced. To generate genetically fixed mutants, they are conventionally allowed to self-pollinate, a procedure which segregates individuals into mutant heterozygotes/homozygotes and wild types. The chances of recovering homozygous mutants among the progeny depend not only on meiotic segregation but also on the frequency of mutated germline cells in the chimeric mother plant. In Nicotiana species, the heritability of Cas9-induced mutations has not been demonstrated yet. RNA-guided Cas9 endonuclease-mediated mutagenesis was targeted to the green fluorescent protein (GFP) gene harbored by a transgenic tobacco line. Upon retransformation using a GFP-specific guide RNA/Cas9 construct, the T0 plants were allowed to either self-pollinate, or were propagated via regeneration from in vitro cultured embryogenic pollen which give rise to haploid/doubled haploid plants or from leaf explants that form plants vegetatively. Single or multiple mutations were detected in 80% of the T0 plants. About half of these mutations proved heritable via selfing. Regeneration from in vitro cultured embryogenic pollen allowed for homozygous mutants to be produced more efficiently than via sexual reproduction. Consequently, embryogenic pollen culture provides a convenient method to rapidly generate a variety of genetically fixed mutants following site-directed mutagenesis. The recovery of a mutation not found among sexually produced and analyzed progeny was shown to be achievable through vegetative plant propagation in vitro, which eventually resulted in heritability when the somatic clones were selfed. In addition, some in-frame mutations were associated with functional attenuation of the target gene rather than its full knock-out. The generation of mutants with compromised rather than abolished gene functionality holds promise for future approaches to the conclusive functional validation of genes which are indispensible for the plant.
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Affiliation(s)
- Sindy Schedel
- Plant Reproductive Biology, Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Stefanie Pencs
- Plant Reproductive Biology, Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Götz Hensel
- Plant Reproductive Biology, Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Andrea Müller
- Plant Reproductive Biology, Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Twan Rutten
- Structural Cell Biology, Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
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Roy S, Das KP. Homologous Recombination Defective Arabidopsis Mutants Exhibit Enhanced Sensitivity to Abscisic Acid. PLoS One 2017; 12:e0169294. [PMID: 28046013 PMCID: PMC5207409 DOI: 10.1371/journal.pone.0169294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/14/2016] [Indexed: 12/27/2022] Open
Abstract
Abscisic acid (ABA) acts as an important plant hormone in regulating various aspects of plant growth and developmental processes particularly under abiotic stress conditions. An increased ABA level in plant cells inhibits DNA replication and cell division, causing plant growth retardation. In this study, we have investigated the effects of ABA on the growth responses of some major loss-of-function mutants of DNA double-stand break (DSB) repair genes in Arabidopsis during seed germination and early stages of seedling growth for understanding the role of ABA in the induction of genome instability in plants. A comparative analysis of ABA sensitivity of wild-type Arabidopsis and the knockout mutant lines related to DSB sensors, including atatm, atatr, the non-homologous end joining (NHEJ) pathway genes, and mutants related to homologous recombination (HR) pathway genes showed relatively enhanced sensitivity of atatr and HR-related mutants to ABA treatment. The expression levels of HR-related genes were increased in wild-type Arabidopsis (Col-0) during seed germination and early stages of seedling growth. Immunoblotting experiments detected phosphorylation of histone H2AX in wild-type (Col-0) and DSB repair gene mutants after ABA treatment, indicating the activation of DNA damage response due to ABA treatment. Analyses of DSB repair kinetics using comet assay under neutral condition have revealed comparatively slower DSB repair activity in HR mutants. Overall, our results have provided comprehensive information on the possible effect of ABA on DNA repair machinery in plants and also indicated potential functional involvement of HR pathway in repairing ABA induced DNA damage in Arabidopsis.
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Affiliation(s)
- Sujit Roy
- Protein Chemistry laboratory, Department of Chemistry, Bose Institute, Kolkata, India
| | - Kali Pada Das
- Protein Chemistry laboratory, Department of Chemistry, Bose Institute, Kolkata, India
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DNA damage checkpoint kinase ATM regulates germination and maintains genome stability in seeds. Proc Natl Acad Sci U S A 2016; 113:9647-52. [PMID: 27503884 DOI: 10.1073/pnas.1608829113] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Genome integrity is crucial for cellular survival and the faithful transmission of genetic information. The eukaryotic cellular response to DNA damage is orchestrated by the DNA damage checkpoint kinases ATAXIA TELANGIECTASIA MUTATED (ATM) and ATM AND RAD3-RELATED (ATR). Here we identify important physiological roles for these sensor kinases in control of seed germination. We demonstrate that double-strand breaks (DSBs) are rate-limiting for germination. We identify that desiccation tolerant seeds exhibit a striking transcriptional DSB damage response during germination, indicative of high levels of genotoxic stress, which is induced following maturation drying and quiescence. Mutant atr and atm seeds are highly resistant to aging, establishing ATM and ATR as determinants of seed viability. In response to aging, ATM delays germination, whereas atm mutant seeds germinate with extensive chromosomal abnormalities. This identifies ATM as a major factor that controls germination in aged seeds, integrating progression through germination with surveillance of genome integrity. Mechanistically, ATM functions through control of DNA replication in imbibing seeds. ATM signaling is mediated by transcriptional control of the cell cycle inhibitor SIAMESE-RELATED 5, an essential factor required for the aging-induced delay to germination. In the soil seed bank, seeds exhibit increased transcript levels of ATM and ATR, with changes in dormancy and germination potential modulated by environmental signals, including temperature and soil moisture. Collectively, our findings reveal physiological functions for these sensor kinases in linking genome integrity to germination, thereby influencing seed quality, crucial for plant survival in the natural environment and sustainable crop production.
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80
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Rocha LC, Mittelmann A, Houben A, Techio VH. Fragile sites of 45S rDNA of Lolium multiflorum are not hotspots for chromosomal breakages induced by X-ray. Mol Biol Rep 2016; 43:659-65. [PMID: 27174104 DOI: 10.1007/s11033-016-4003-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/04/2016] [Indexed: 01/24/2023]
Abstract
Sites of 45S rDNA of Lolium are regions denominated fragile sites (FSs), constituting regions slightly stained with DAPI due to increased DNA unpacking in metaphasic chromosomes. Considered to be fragile regions in the genome, the FSs might be more responsive to induced breaks and result in chromosomal fragments and rearrangements, unless repairing mechanisms such as recombination or de novo telomere formation play a role at the break site of the DNA. Thus, this study aimed at investigating if SFs from Lolium are hotspots for the occurrence of breakages induced by X-ray and if they are regions favorable to synthesize new telomeres, using Hordeum vulgare as a comparative model. Lolium multiflorum and H. vulgare seedlings were irradiated with 20 and 50 Gy X-ray and evaluated one day following the irradiation and at 7-days intervals for a 28-days period, using FISH technique with 45S rDNA and Arabidopsis-type telomere probes in order to investigate the presence of chromosomal breakages and new telomere formation. H. vulgare did not survive after a few days of irradiation due to the increased rate of abnormalities. L. multiflorum also exhibited chromosomal abnormalities following the exposure, yet over the 28-days trial it had a decrease in the chromosomal damage rate and formation of de novo telomere has not been detected along this time. Despite being considered to be fragile regions in the genome, the 45S rDNA sites of Lolium are not hotspots to chromosomal breakages after the induction of breakages.
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Affiliation(s)
- Laiane Corsini Rocha
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | - Andrea Mittelmann
- Embrapa Dairy Cattle/Embrapa Temperate Agriculture, Juiz de Fora/Pelotas, Minas Gerais State/Rio Grande do Sul State, Brazil
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, StadtSeeland, Germany.
| | - Vânia Helena Techio
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil.
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81
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Salo HM, Sarjala T, Jokela A, Häggman H, Vuosku J. Moderate stress responses and specific changes in polyamine metabolism characterize Scots pine somatic embryogenesis. TREE PHYSIOLOGY 2016; 36:392-402. [PMID: 26786537 PMCID: PMC4885945 DOI: 10.1093/treephys/tpv136] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 11/29/2015] [Indexed: 05/02/2023]
Abstract
Somatic embryogenesis (SE) is one of the methods with the highest potential for the vegetative propagation of commercially important coniferous species. However, many conifers, including Scots pine (Pinus sylvestris L.), are recalcitrant to SE and a better understanding of the mechanisms behind the SE process is needed. In Scots pine SE cultures, embryo production is commonly induced by the removal of auxin, addition of abscisic acid (ABA) and the desiccation of cell masses by polyethylene glycol (PEG). In the present study, we focus on the possible link between the induction of somatic embryo formation and cellular stress responses such as hydrogen peroxide protection, DNA repair, changes in polyamine (PA) metabolism and autophagy. Cellular PA contents and the expression of the PA metabolism genes arginine decarboxylase (ADC), spermidine synthase (SPDS), thermospermine synthase (ACL5) and diamine oxidase (DAO) were analyzed, as well as the expression of catalase (CAT), DNA repair genes (RAD51, KU80) and autophagy-related genes (ATG5, ATG8) throughout the induction of somatic embryo formation in Scots pine SE cultures. Among the embryo-producing SE lines, the expression of ADC, SPDS, ACL5, DAO, CAT, RAD51, KU80 and ATG8 showed consistent profiles. Furthermore, the overall low expression of the stress-related genes suggests that cells in those SE lines were not stressed but recognized the ABA+PEG treatment as a signal to trigger the embryogenic pathway. In those SE lines that were unable to produce embryos, cells seemed to experience the ABA+PEG treatment mostly as osmotic stress and activated a wide range of stress defense mechanisms. Altogether, our results suggest that the direction to the embryogenic pathway is connected with cellular stress responses in Scots pine SE cultures. Thus, the manipulation of stress response pathways may provide a way to enhance somatic embryo production in recalcitrant Scots pine SE lines.
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Affiliation(s)
- Heikki M Salo
- Genetics and Physiology Department, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
| | - Tytti Sarjala
- Natural Resources Institute Finland (Luke), Parkano Unit, FI-39700 Parkano, Finland
| | - Anne Jokela
- Genetics and Physiology Department, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
| | - Hely Häggman
- Genetics and Physiology Department, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
| | - Jaana Vuosku
- Genetics and Physiology Department, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland Natural Resources Institute Finland (Luke), Rovaniemi Unit, FI-96300 Rovaniemi, Finland
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82
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Aklilu BB, Culligan KM. Molecular Evolution and Functional Diversification of Replication Protein A1 in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:33. [PMID: 26858742 PMCID: PMC4731521 DOI: 10.3389/fpls.2016.00033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/10/2016] [Indexed: 05/23/2023]
Abstract
Replication protein A (RPA) is a heterotrimeric, single-stranded DNA binding complex required for eukaryotic DNA replication, repair, and recombination. RPA is composed of three subunits, RPA1, RPA2, and RPA3. In contrast to single RPA subunit genes generally found in animals and yeast, plants encode multiple paralogs of RPA subunits, suggesting subfunctionalization. Genetic analysis demonstrates that five Arabidopsis thaliana RPA1 paralogs (RPA1A to RPA1E) have unique and overlapping functions in DNA replication, repair, and meiosis. We hypothesize here that RPA1 subfunctionalities will be reflected in major structural and sequence differences among the paralogs. To address this, we analyzed amino acid and nucleotide sequences of RPA1 paralogs from 25 complete genomes representing a wide spectrum of plants and unicellular green algae. We find here that the plant RPA1 gene family is divided into three general groups termed RPA1A, RPA1B, and RPA1C, which likely arose from two progenitor groups in unicellular green algae. In the family Brassicaceae the RPA1B and RPA1C groups have further expanded to include two unique sub-functional paralogs RPA1D and RPA1E, respectively. In addition, RPA1 groups have unique domains, motifs, cis-elements, gene expression profiles, and pattern of conservation that are consistent with proposed functions in monocot and dicot species, including a novel C-terminal zinc-finger domain found only in plant RPA1C-like sequences. These results allow for improved prediction of RPA1 subunit functions in newly sequenced plant genomes, and potentially provide a unique molecular tool to improve classification of Brassicaceae species.
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Affiliation(s)
- Behailu B. Aklilu
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
- Program in Genetics, University of New HampshireDurham, NH, USA
| | - Kevin M. Culligan
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
- Program in Genetics, University of New HampshireDurham, NH, USA
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83
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Kumar S, Barone P, Smith M. Gene targeting and transgene stacking using intra genomic homologous recombination in plants. PLANT METHODS 2016; 12:11. [PMID: 26839580 PMCID: PMC4736180 DOI: 10.1186/s13007-016-0111-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/14/2016] [Indexed: 05/04/2023]
Abstract
Modern agriculture has created a demand for plant biotechnology products that provide durable resistance to insect pests, tolerance of herbicide applications for weed control, and agronomic traits tailored for specific geographies. These transgenic trait products require a modular and sequential multigene stacking platform that is supported by precise genome engineering technology. Designed nucleases have emerged as potent tools for creating targeted DNA double strand breaks (DSBs). Exogenously supplied donor DNA can repair the targeted DSB by a process known as gene targeting (GT), resulting in a desired modification of the target genome. The potential of GT technology has not been fully realized for trait deployment in agriculture, mainly because of inefficient transformation and plant regeneration systems in a majority of crop plants and genotypes. This challenge of transgene stacking in plants could be overcome by Intra-Genomic Homologous Recombination (IGHR) that converts independently segregating unlinked donor and target transgenic loci into a genetically linked molecular stack. The method requires stable integration of the donor DNA into the plant genome followed by intra-genomic mobilization. IGHR complements conventional breeding with genetic transformation and designed nucleases to provide a flexible transgene stacking and trait deployment platform.
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Affiliation(s)
- Sandeep Kumar
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46286 USA
| | - Pierluigi Barone
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46286 USA
| | - Michelle Smith
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46286 USA
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84
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Kleinboelting N, Huep G, Appelhagen I, Viehoever P, Li Y, Weisshaar B. The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism. MOLECULAR PLANT 2015; 8:1651-64. [PMID: 26343971 DOI: 10.1016/j.molp.2015.08.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/28/2015] [Accepted: 08/13/2015] [Indexed: 05/06/2023]
Abstract
Transformation by Agrobacterium tumefaciens, an important tool in modern plant research, involves the integration of T-DNA initially present on a plasmid in agrobacteria into the genome of plant cells. The process of attachment of the agrobacteria to plant cells and the transport of T-DNA into the cell and further to the nucleus has been well described. However, the exact mechanism of integration into the host's DNA is still unclear, although several models have been proposed. During confirmation of T-DNA insertion alleles from the GABI-Kat collection of Arabidopsis thaliana mutants, we have generated about 34,000 sequences from the junctions between inserted T-DNA and adjacent genome regions. Here, we describe the evaluation of this dataset with regard to existing models for T-DNA integration. The results suggest that integration into the plant genome is mainly mediated by the endogenous plant DNA repair machinery. The observed integration events showed characteristics highly similar to those of repair sites of double-strand breaks with respect to microhomology and deletion sizes. In addition, we describe unexpected integration events, such as large deletions and inversions at the integration site that are relevant for correct interpretation of results from T-DNA insertion mutants in reverse genetics experiments.
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Affiliation(s)
- Nils Kleinboelting
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Gunnar Huep
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Ingo Appelhagen
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Prisca Viehoever
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Yong Li
- Department of Medicine IV, University Hospital Freiburg, Berliner Allee 29, 79110 Freiburg, Germany
| | - Bernd Weisshaar
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.
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85
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Waterworth WM, Drury GE, Blundell-Hunter G, West CE. Arabidopsis TAF1 is an MRE11-interacting protein required for resistance to genotoxic stress and viability of the male gametophyte. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:545-57. [PMID: 26358508 PMCID: PMC4949998 DOI: 10.1111/tpj.13020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 05/07/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) by recombination pathways is essential for plant growth and fertility. The recombination endonuclease MRE11 plays important roles in sensing and repair of DNA DSBs. Here we demonstrate protein interaction between Arabidopsis MRE11 and the histone acetyltransferase TAF1, a TATA-binding protein Associated Factor (TAF) of the RNA polymerase II transcription initiation factor complex TFIID. Arabidopsis has two TAF1 homologues termed TAF1 and TAF1b and mutant taf1b lines are viable and fertile. In contrast, taf1 null mutations are lethal, demonstrating that TAF1 is an essential gene. Heterozygous taf1+/- plants display abnormal segregation of the mutant allele resulting from defects in pollen tube development, indicating that TAF1 is important for gamete viability. Characterization of an allelic series of taf1 lines revealed that hypomorphic mutants are viable but display developmental defects and reduced plant fertility. Hypersensitivity of taf1 mutants lacking the C-terminal bromodomain to X-rays and mitomycin C, but not to other forms of abiotic stress, established a specific role for TAF1 in plant DNA repair processes. Collectively these studies reveal a function for TAF1 in plant resistance to genotoxic stress, providing further insight into the molecular mechanisms of the DNA damage response in plants.
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Affiliation(s)
- Wanda M Waterworth
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Georgina E Drury
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | | | - Christopher E West
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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86
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Zhang H, Gu Z, Wu Q, Yang L, Liu C, Ma H, Xia Y, Ge X. Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation. Sci Rep 2015; 5:15892. [PMID: 26516022 PMCID: PMC4626836 DOI: 10.1038/srep15892] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 10/05/2015] [Indexed: 12/28/2022] Open
Abstract
Poly(ADP-ribosyl)ation is a reversible post-translational modification of proteins, characterized by the addition of poly(ADP-ribose) (PAR) to proteins by poly(ADP-ribose) polymerase (PARP), and removal of PAR by poly(ADP-ribose) glycohydrolase (PARG). Three PARPs and two PARGs have been found in Arabidopsis, but their respective roles are not fully understood. In this study, the functions of each PARP and PARG in DNA repair were analyzed based on their mutant phenotypes under genotoxic stresses. Double or triple mutant analysis revealed that PARP1 and PARP2, but not PARP3, play a similar but not critical role in DNA repair in Arabidopsis seedlings. PARG1 and PARG2 play an essential and a minor role, respectively under the same conditions. Mutation of PARG1 results in increased DNA damage level and enhanced cell death in plants after bleomycin treatment. PARG1 expression is induced primarily in root and shoot meristems by bleomycin and induction of PARG1 is dependent on ATM and ATR kinases. PARG1 also antagonistically modulates the DNA repair process by preventing the over-induction of DNA repair genes. Our study determined the contribution of each PARP and PARG member in DNA repair and indicated that PARG1 plays a critical role in this process.
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Affiliation(s)
- Hailei Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Department of Biochemistry and Molecular Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zongying Gu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Department of Biochemistry and Molecular Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiao Wu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Department of Biochemistry and Molecular Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lifeng Yang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Department of Biochemistry and Molecular Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Caifeng Liu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Department of Biochemistry and Molecular Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Department of Biochemistry and Molecular Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, China
| | - Xiaochun Ge
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Department of Biochemistry and Molecular Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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87
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Manova V, Gruszka D. DNA damage and repair in plants - from models to crops. FRONTIERS IN PLANT SCIENCE 2015; 6:885. [PMID: 26557130 PMCID: PMC4617055 DOI: 10.3389/fpls.2015.00885] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 10/05/2015] [Indexed: 05/17/2023]
Abstract
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited. However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis. Moreover, abnormalities in DNA repair which proved to be lethal for animal models are tolerated in plant genomes, although sensitivity to DNA damaging agents is retained. Due to the high conservation of DNA repair processes and factors mediating them among eukaryotes, genes and proteins that have been identified in model species may serve to identify homologous sequences in other species, including crop plants, in which these mechanisms are poorly understood. Crop breeding programs have provided remarkable advances in food quality and yield over the last century. Although the human population is predicted to "peak" by 2050, further advances in yield will be required to feed this population. Breeding requires genetic diversity. The biological impact of any mutagenic agent used for the creation of genetic diversity depends on the chemical nature of the induced lesions and on the efficiency and accuracy of their repair. More recent targeted mutagenesis procedures also depend on host repair processes, with different pathways yielding different products. Enhanced understanding of DNA repair processes in plants will inform and accelerate the engineering of crop genomes via both traditional and targeted approaches.
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Affiliation(s)
- Vasilissa Manova
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of SciencesSofia
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of SilesiaKatowice, Poland
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88
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Murgia I, Giacometti S, Balestrazzi A, Paparella S, Pagliano C, Morandini P. Analysis of the transgenerational iron deficiency stress memory in Arabidopsis thaliana plants. FRONTIERS IN PLANT SCIENCE 2015; 6:745. [PMID: 26442058 PMCID: PMC4585125 DOI: 10.3389/fpls.2015.00745] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/31/2015] [Indexed: 05/23/2023]
Abstract
We investigated the existence of the transgenerational memory of iron (Fe) deficiency stress, in Arabidopsis thaliana. Plants were grown under Fe deficiency/sufficiency, and so were their offspring. The frequency of somatic homologous recombination (SHR) events, of DNA strand breaks as well as the expression of the transcription elongation factor TFIIS-like gene increase when plants are grown under Fe deficiency. However, SHR frequency, DNA strand break events, and TFIIS-like gene expression do not increase further when plants are grown for more than one generation under the same stress, and furthermore, they decrease back to control values within two succeeding generations grown under control conditions, regardless of the Fe deficiency stress history of the mother plants. Seedlings produced from plants grown under Fe deficiency evolve more oxygen than control seedlings, when grown under Fe sufficiency: however, this trait is not associated with any change in the protein profile of the photosynthetic apparatus and is not transmitted to more than one generation. Lastly, plants grown for multiple generations under Fe deficiency produce seeds with greater longevity: however, this trait is not inherited in offspring generations unexposed to stress. These findings suggest the existence of multiple-step control of mechanisms to prevent a genuine and stable transgenerational transmission of Fe deficiency stress memory, with the tightest control on DNA integrity.
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Affiliation(s)
- Irene Murgia
- Department of Biosciences, University of MilanoMilano, Italy
| | | | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of PaviaPavia, Italy
| | - Stefania Paparella
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of PaviaPavia, Italy
| | - Cristina Pagliano
- Applied Science and Technology Department – BioSolar Lab, Polytechnic University of TurinAlessandria, Italy
| | - Piero Morandini
- Department of Biosciences, University of MilanoMilano, Italy
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Paparella S, Araújo SS, Rossi G, Wijayasinghe M, Carbonera D, Balestrazzi A. Seed priming: state of the art and new perspectives. PLANT CELL REPORTS 2015; 34:1281-93. [PMID: 25812837 DOI: 10.1007/s00299-015-1784-y] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/15/2015] [Accepted: 03/16/2015] [Indexed: 05/18/2023]
Abstract
Priming applied to commercial seed lots is widely used by seed technologists to enhance seed vigour in terms of germination potential and increased stress tolerance. Priming can be also valuable to seed bank operators who need improved protocols of ex situ conservation of germplasm collections (crop and native species). Depending on plant species, seed morphology and physiology, different priming treatments can be applied, all of them triggering the so-called 'pre-germinative metabolism'. This physiological process takes place during early seed imbibition and includes the seed repair response (activation of DNA repair pathways and antioxidant mechanisms), essential to preserve genome integrity, ensuring proper germination and seedling development. The review provides an overview of priming technology, describing the range of physical-chemical and biological treatments currently available. Optimised priming protocols can be designed using the 'hydrotime concept' analysis which provides the theoretical bases for assessing the relationship between water potential and germination rate. Despite the efforts so far reported to further improve seed priming, novel ideas and cutting-edge investigations need to be brought into this technological sector of agri-seed industry. Multidisciplinary translational research combining digital, bioinformatic and molecular tools will significantly contribute to expand the range of priming applications to other relevant commercial sectors, e.g. the native seed market.
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Affiliation(s)
- S Paparella
- Department of Biology and Biotechnology 'L. Spallanzani', via Ferrata 1, 27100, Pavia, Italy
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90
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DNA double-strand breaks alter the spatial arrangement of homologous loci in plant cells. Sci Rep 2015; 5:11058. [PMID: 26046331 PMCID: PMC4457028 DOI: 10.1038/srep11058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/11/2015] [Indexed: 12/31/2022] Open
Abstract
Chromatin dynamics and arrangement are involved in many biological processes in nuclei of eukaryotes including plants. Plants have to respond rapidly to various environmental stimuli to achieve growth and development because they cannot move. It is assumed that the alteration of chromatin dynamics and arrangement support the response to these stimuli; however, there is little information in plants. In this study, we investigated the chromatin dynamics and arrangement with DNA damage in Arabidopsis thaliana by live-cell imaging with the lacO/LacI-EGFP system and simulation analysis. It was revealed that homologous loci kept a constant distance in nuclei of A. thaliana roots in general growth. We also found that DNA double-strand breaks (DSBs) induce the approach of the homologous loci with γ-irradiation. Furthermore, AtRAD54, which performs an important role in the homologous recombination repair pathway, was involved in the pairing of homologous loci with γ-irradiation. These results suggest that homologous loci approach each other to repair DSBs, and AtRAD54 mediates these phenomena.
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91
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Waterworth WM, Bray CM, West CE. The importance of safeguarding genome integrity in germination and seed longevity. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3549-58. [PMID: 25750428 DOI: 10.1093/jxb/erv080] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Seeds are important to agriculture and conservation of plant biodiversity. In agriculture, seed germination performance is an important determinant of crop yield, in particular under adverse climatic conditions. Deterioration in seed quality is associated with the accumulation of cellular damage to macromolecules including lipids, protein, and DNA. Mechanisms that mitigate the deleterious cellular damage incurred in the quiescent state and in cycles of desiccation-hydration are crucial for the maintenance of seed viability and germination vigour. In early-imbibing seeds, damage to the embryo genome must be repaired prior to initiation of cell division to minimize growth inhibition and mutation of genetic information. Here we review recent advances that have established molecular links between genome integrity and seed quality. These studies identified that maintenance of genome integrity is particularly important to the seed stage of the plant lifecycle, revealing new insight into the physiological roles of plant DNA repair and recombination mechanisms. The high conservation of DNA repair and recombination factors across plant species underlines their potential as promising targets for the improvement of crop performance and development of molecular markers for prediction of seed vigour.
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Affiliation(s)
| | - Clifford M Bray
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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92
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Oliveira TM, da Silva FR, Bonatto D, Neves DM, Morillon R, Maserti BE, Filho MAC, Costa MGC, Pirovani CP, Gesteira AS. Comparative study of the protein profiles of Sunki mandarin and Rangpur lime plants in response to water deficit. BMC PLANT BIOLOGY 2015; 15:69. [PMID: 25849288 PMCID: PMC4355367 DOI: 10.1186/s12870-015-0416-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/06/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Rootstocks play a major role in the tolerance of citrus plants to water deficit by controlling and adjusting the water supply to meet the transpiration demand of the shoots. Alterations in protein abundance in citrus roots are crucial for plant adaptation to water deficit. We performed two-dimensional electrophoresis (2-DE) separation followed by LC/MS/MS to assess the proteome responses of the roots of two citrus rootstocks, Rangpur lime (Citrus limonia Osbeck) and 'Sunki Maravilha' (Citrus sunki) mandarin, which show contrasting tolerances to water deficits at the physiological and molecular levels. RESULTS Changes in the abundance of 36 and 38 proteins in Rangpur lime and 'Sunki Maravilha' mandarin, respectively, were observed via LC/MS/MS in response to water deficit. Multivariate principal component analysis (PCA) of the data revealed major changes in the protein profile of 'Sunki Maravilha' in response to water deficit. Additionally, proteomics and systems biology analyses allowed for the general elucidation of the major mechanisms associated with the differential responses to water deficit of both varieties. The defense mechanisms of Rangpur lime included changes in the metabolism of carbohydrates and amino acids as well as in the activation of reactive oxygen species (ROS) detoxification and in the levels of proteins involved in water stress defense. In contrast, the adaptation of 'Sunki Maravilha' to stress was aided by the activation of DNA repair and processing proteins. CONCLUSIONS Our study reveals that the levels of a number of proteins involved in various cellular pathways are affected during water deficit in the roots of citrus plants. The results show that acclimatization to water deficit involves specific responses in Rangpur lime and 'Sunki Maravilha' mandarin. This study provides insights into the effects of drought on the abundance of proteins in the roots of two varieties of citrus rootstocks. In addition, this work allows for a better understanding of the molecular basis of the response to water deficit in citrus. Further analysis is needed to elucidate the behaviors of the key target proteins involved in this response.
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Affiliation(s)
- Tahise M Oliveira
- />Universidade Estadual de Santa Cruz-UESC, Rodovia Ilhéus-Itabuna, Km 16, Salobrinho, Bahia Brazil
| | - Fernanda R da Silva
- />Centro de Biotecnologia, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul-UFGRS, Avenida Bento Goncalves, 9500 Porto Alegre, Rio Grande do Sul Brazil
| | - Diego Bonatto
- />Centro de Biotecnologia, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul-UFGRS, Avenida Bento Goncalves, 9500 Porto Alegre, Rio Grande do Sul Brazil
| | - Diana M Neves
- />Universidade Estadual de Santa Cruz-UESC, Rodovia Ilhéus-Itabuna, Km 16, Salobrinho, Bahia Brazil
| | - Raphael Morillon
- />IVIA; Centro de Genomica, Ctra. Moncada-Náquera Km 5, 46113 Moncada, Valencia Spain
- />CIRAD, UMR AGAP, Avenue Agropolis - TA A-75/02 – 34398, Montpellier Cedex 5, France
| | - Bianca E Maserti
- />Dipartimento di Scienze BioAgroAlimentari, CNR-IPSP, Istituto per la Protezione Sostenibile delle Piante, Area della Ricerca CNR, Via Madonna del Piano 10, Via Madonna del Piano n 10, 50019 Sesto Fiorentino, FI Italy
| | | | - Marcio GC Costa
- />Universidade Estadual de Santa Cruz-UESC, Rodovia Ilhéus-Itabuna, Km 16, Salobrinho, Bahia Brazil
| | - Carlos P Pirovani
- />Universidade Estadual de Santa Cruz-UESC, Rodovia Ilhéus-Itabuna, Km 16, Salobrinho, Bahia Brazil
| | - Abelmon S Gesteira
- />Embrapa Mandioca e Fruticultura, Rua Embrapa, s/n, Cruz das Almas, 44380-000 Bahia Brazil
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93
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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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94
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DNA damage and repair in plants under ultraviolet and ionizing radiations. ScientificWorldJournal 2015; 2015:250158. [PMID: 25729769 PMCID: PMC4333283 DOI: 10.1155/2015/250158] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/27/2014] [Accepted: 11/04/2014] [Indexed: 11/17/2022] Open
Abstract
Being sessile, plants are continuously exposed to DNA-damaging agents present in the environment such as ultraviolet (UV) and ionizing radiations (IR). Sunlight acts as an energy source for photosynthetic plants; hence, avoidance of UV radiations (namely, UV-A, 315–400 nm; UV-B, 280–315 nm; and UV-C, <280 nm) is unpreventable. DNA in particular strongly absorbs UV-B; therefore, it is the most important target for UV-B induced damage. On the other hand, IR causes water radiolysis, which generates highly reactive hydroxyl radicals (OH•) and causes radiogenic damage to important cellular components. However, to maintain genomic integrity under UV/IR exposure, plants make use of several DNA repair mechanisms. In the light of recent breakthrough, the current minireview (a) introduces UV/IR and overviews UV/IR-mediated DNA damage products and (b) critically discusses the biochemistry and genetics of major pathways responsible for the repair of UV/IR-accrued DNA damage. The outcome of the discussion may be helpful in devising future research in the current context.
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95
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Rissel D, Losch J, Peiter E. The nuclear protein Poly(ADP-ribose) polymerase 3 (AtPARP3) is required for seed storability in Arabidopsis thaliana. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:1058-64. [PMID: 24533577 DOI: 10.1111/plb.12167] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 01/21/2014] [Indexed: 05/21/2023]
Abstract
The deterioration of seeds during prolonged storage results in a reduction of viability and germination rate. DNA damage is one of the major cellular defects associated with seed deterioration. It is provoked by the formation of reactive oxygen species (ROS) even in the quiescent state of the desiccated seed. In contrast to other stages of seed life, DNA repair during storage is hindered through the low seed water content; thereby DNA lesions can accumulate. To allow subsequent seedling development, DNA repair has thus to be initiated immediately upon imbibition. Poly(ADP-ribose) polymerases (PARPs) are important components in the DNA damage response in humans. Arabidopsis thaliana contains three homologues to the human HsPARP1 protein. Of these three, only AtPARP3 was very highly expressed in seeds. Histochemical GUS staining of embryos and endosperm layers revealed strong promoter activity of AtPARP3 during all steps of germination. This coincided with high ROS activity and indicated a role of the nuclear-localised AtPARP3 in DNA repair during germination. Accordingly, stored parp3-1 mutant seeds lacking AtPARP3 expression displayed a delay in germination as compared to Col-0 wild-type seeds. A controlled deterioration test showed that the mutant seeds were hypersensitive to unfavourable storage conditions. The results demonstrate that AtPARP3 is an important component of seed storability and viability.
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Affiliation(s)
- D Rissel
- Plant Nutrition Laboratory, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences (IAEW), Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany; Agrochemisches Institut Piesteritz e.V., Lutherstadt Wittenberg, Germany
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96
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Dong CB, Mao JF, Suo YJ, Shi L, Wang J, Zhang PD, Kang XY. A strategy for characterization of persistent heteroduplex DNA in higher plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:282-291. [PMID: 25073546 DOI: 10.1111/tpj.12631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus-centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.
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Affiliation(s)
- Chun-Bo Dong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
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97
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Yoshimura K, Ogawa T, Tsujimura M, Ishikawa K, Shigeoka S. Ectopic expression of the human MutT-type Nudix hydrolase, hMTH1, confers enhanced tolerance to oxidative stress in arabidopsis. PLANT & CELL PHYSIOLOGY 2014; 55:1534-1543. [PMID: 24928220 DOI: 10.1093/pcp/pcu083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Oxidized nucleotides produced by oxidative stress cause DNA mutations and the production of abnormal proteins. Thus, mammalian cells have developed multiple MutT-type Nudix hydrolases that exhibit pyrophosphohydrolase activity toward oxidized nucleotides in the cytosol, mitochondria and nucleus. On the other hand, AtNUDX1 is the only MutT-type Nudix hydrolase in the cytosol of Arabidopsis plants. To clarify the physiological significance of the defenses against oxidatively induced DNA damage in plant organelles, we analyzed the effects of the ectopic expression of the human MutT-type Nudix hydrolase, hMTH1, which was localized in the cytosol (cyt-hMTH1), chloroplasts (chl-hMTH1) and mitochondria (mit-hMTH1) of Arabidopsis cells, on tolerance to oxidative stress. Tolerance to oxidative stress caused by heating and paraquat (PQ) treatment was higher in the mit-hMTH1 and chl-hMTH1 plants than in the control and cyt-hMTH1 plants. The accumulation of H2O2 and the frequency of dead cells were lower in the mit-hMTH1 and chl-hMTH1 plants under stressful conditions. The poly(ADP-ribosyl)ation (PAR) reaction, which regulates repair systems for damaged DNA, was activated in the mit-hMTH1 and chl-hMTH1 plants under heat stress and PQ treatment. Furthermore, DNA fragmentation, which caused programmed cell death, was clearly suppressed in the mit-hMTH1 and chl-hMTH1 plants under heat stress. These results demonstrated that the ectopic expression of hMTH1 in the chloroplasts and mitochondria of Arabidopsis enhanced oxidative stress tolerance by activating the PAR reaction and suppressing programmed cell death.
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Affiliation(s)
- Kazuya Yoshimura
- Department of Food and Nutritional Science, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Takahisa Ogawa
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara, 631-8505 Japan
| | - Masaki Tsujimura
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara, 631-8505 Japan
| | - Kazuya Ishikawa
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara, 631-8505 Japan
| | - Shigeru Shigeoka
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara, 631-8505 Japan
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98
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Characterization of DNA repair deficient strains of Chlamydomonas reinhardtii generated by insertional mutagenesis. PLoS One 2014; 9:e105482. [PMID: 25144319 PMCID: PMC4140758 DOI: 10.1371/journal.pone.0105482] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/23/2014] [Indexed: 12/15/2022] Open
Abstract
While the mechanisms governing DNA damage response and repair are fundamentally conserved, cross-kingdom comparisons indicate that they differ in many aspects due to differences in life-styles and developmental strategies. In photosynthetic organisms these differences have not been fully explored because gene-discovery approaches are mainly based on homology searches with known DDR/DNA repair proteins. Here we performed a forward genetic screen in the green algae Chlamydomonas reinhardtii to identify genes deficient in DDR/DNA repair. We isolated five insertional mutants that were sensitive to various genotoxic insults and two of them exhibited altered efficiency of transgene integration. To identify genomic regions disrupted in these mutants, we established a novel adaptor-ligation strategy for the efficient recovery of the insertion flanking sites. Four mutants harbored deletions that involved known DNA repair factors, DNA Pol zeta, DNA Pol theta, SAE2/COM1, and two neighbouring genes encoding ERCC1 and RAD17. Deletion in the last mutant spanned two Chlamydomonas-specific genes with unknown function, demonstrating the utility of this approach for discovering novel factors involved in genome maintenance.
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99
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Stress induces cell dedifferentiation in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:378-84. [PMID: 25086338 DOI: 10.1016/j.bbagrm.2014.07.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 12/14/2022]
Abstract
Accumulating evidence lends support to the proposal that a major theme in plant responses to stresses is dedifferentiation, whereby mature cells acquire stem cell features (e.g. open chromatin conformation) prior to acquisition of a new cell fate. In this review, we discuss data addressing plant cell plasticity and provide evidence linking stress, dedifferentiation and a switch in cell fate. We emphasize the epigenetic modifications associated with stress-induced global changes in chromatin structure and conclude with the implications for genetic variation and for induced pluripotent stem cells in animals. It appears that stress is perceived as a signal that directs plant cells to undergo reprogramming (dedifferentiation) as a means for adaptation and in preparation for a stimulus-based acquisition of a new cell fate. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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100
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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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