51
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Affiliation(s)
- Seisuke Kimura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda-shi, Chiba, Japan
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52
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da Costa-Nunes JA, Bhatt AM, O'Shea S, West CE, Bray CM, Grossniklaus U, Dickinson HG. Characterization of the three Arabidopsis thaliana RAD21 cohesins reveals differential responses to ionizing radiation. JOURNAL OF EXPERIMENTAL BOTANY 2006; 57:971-83. [PMID: 16488915 DOI: 10.1093/jxb/erj083] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The RAD21/REC8 gene family has been implicated in sister chromatid cohesion and DNA repair in several organisms. Unlike most eukaryotes, Arabidopsis thaliana has three RAD21 gene homologues, and their cloning and characterization are reported here. All three genes, AtRAD21.1, AtRAD21.2, and AtRAD21.3, are expressed in tissues rich in cells undergoing cell division, and AtRAD21.3 shows the highest relative level of expression. An increase in steady-state levels of AtRAD21.1 transcript was also observed, specifically after the induction of DNA damage. Phenotypic analysis of the atrad21.1 and atrad21.3 mutants revealed that neither of the single mutants was lethal, probably due to the redundancy in function of the AtRAD21 genes. However, AtRAD21.1 plays a critical role in recovery from DNA damage during seed imbibition, prior to germination, as atrad21.1 mutant seeds are hypersensitive to radiation damage.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/physiology
- Arabidopsis/radiation effects
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Arabidopsis Proteins/physiology
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/physiology
- Cloning, Molecular
- DNA Damage
- Flowers/anatomy & histology
- Flowers/physiology
- Flowers/radiation effects
- Gene Expression Regulation, Plant
- Genes, Plant
- Genes, Reporter
- Molecular Sequence Data
- Mutation
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Nuclear Proteins/physiology
- Phenotype
- RNA, Messenger/metabolism
- Radiation, Ionizing
- Seedlings/anatomy & histology
- Seedlings/physiology
- Seedlings/radiation effects
- Seeds/anatomy & histology
- Seeds/physiology
- Seeds/radiation effects
- Sequence Analysis, Protein
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- J A da Costa-Nunes
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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53
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Bray CM, West CE. DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity. THE NEW PHYTOLOGIST 2005; 168:511-28. [PMID: 16313635 DOI: 10.1111/j.1469-8137.2005.01548.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As obligate phototrophs, plants harness energy from sunlight to split water, producing oxygen and reducing power. This lifestyle exposes plants to particularly high levels of genotoxic stress that threatens genomic integrity, leading to mutation, developmental arrest and cell death. Plants, which with algae are the only photosynthetic eukaryotes, have evolved very effective pathways for DNA damage signalling and repair, and this review summarises our current understanding of these processes in the responses of plants to genotoxic stress. We also identify how the use of new and emerging technologies can complement established physiological and ecological studies to progress the application of this knowledge in biotechnology.
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Affiliation(s)
- Clifford M Bray
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
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54
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Gallego ME, White CI. DNA repair and recombination functions in Arabidopsis telomere maintenance. Chromosome Res 2005; 13:481-91. [PMID: 16132813 DOI: 10.1007/s10577-005-0995-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this review, we discuss recent advances in the knowledge of plant telomere maintenance, focusing on the model plant Arabidopsis thaliana and, in particular, on the roles of proteins involved in DNA repair and recombination. The question of the interrelationships between DNA repair and recombination pathways and proteins with telomere function and maintenance is of increasing interest and has been the subject of a number of recent reviews (Cech 2004, d'Adda di Fagagna et al. 2004, Hande 2004, Harrington 2004, Maser and DePinho 2004). Understanding of telomere biology, DNA repair and recombination in plants has rapidly progressed over the last decade, substantially due to genetic approaches in Arabidopsis, and we feel that this is an appropriate time to review current knowledge in this field. A number of recent reviews have dealt more generally with the subject of plant telomere structure and evolution (Riha et al. 2001, McKnight et al. 2002, Riha and Shippen 2003b, McKnight and Shippen 2004, Fajkus et al. 2005) and we thus focus specifically on plant telomere biology in the context of DNA repair and recombination in Arabidopsis.
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Affiliation(s)
- Maria E Gallego
- UMR 6547 CNRS, Université Blaise Pascal, 24 avenue des Landais, 63177 Aubière, France
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55
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Bleuyard JY, Gallego ME, White CI. Recent advances in understanding of the DNA double-strand break repair machinery of plants. DNA Repair (Amst) 2005; 5:1-12. [PMID: 16202663 DOI: 10.1016/j.dnarep.2005.08.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 08/22/2005] [Accepted: 08/22/2005] [Indexed: 11/21/2022]
Abstract
Living cells suffer numerous and varied alterations of their genetic material. Of these, the DNA double-strand break (DSB) is both particularly threatening and common. Double-strand breaks arise from exposure to DNA damaging agents, but also from cell metabolism-in a fortuitous manner during DNA replication or repair of other kinds of lesions and in a programmed manner, for example during meiosis or V(D)J gene rearrangement. Cells possess several overlapping repair pathways to deal with these breaks, generally designated as genetic recombination. Genetic and biochemical studies have provided considerable amounts of data about the proteins involved in recombination processes and their functions within these processes. Although they have long played a key role in building understanding of genetics, relatively little is known at the molecular level of the genetic recombination processes in plants. The use of reverse genetic approaches and the public availability of sequence tagged mutants in Arabidopsis thaliana have led to increasingly rapid progress in this field over recent years. The rapid progress of studies of recombination in plants is obviously not limited to the DSB repair machinery as such and we ask readers to understand that in order to maintain the focus and to rest within a reasonable length, we present only limited discussion of the exciting advances in the of plant meiosis field, which require a full review in their own right . We thus present here an update on recent advances in understanding of the DSB repair machinery of plants, focussing on Arabidopsis and making a particular effort to place these in the context of more general of understanding of these processes.
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Affiliation(s)
- Jean-Yves Bleuyard
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK.
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56
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Bonatto D, Brendel M, Henriques JAP. A new group of plant-specific ATP-dependent DNA ligases identified by protein phylogeny, hydrophobic cluster analysis and 3-dimensional modelling. FUNCTIONAL PLANT BIOLOGY : FPB 2005; 32:161-174. [PMID: 32689120 DOI: 10.1071/fp04143] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Accepted: 01/06/2005] [Indexed: 06/11/2023]
Abstract
The eukaryotic ATP-dependent DNA ligases comprise a group of orthologous proteins that have distinct roles in DNA metabolism. In contrast with the well-known DNA ligases of animal cells, the DNA ligases of plant cells are poorly described. Until now, only two DNA ligases (I and IV) genes of Arabidopsis thaliana (L.) Heynh were isolated and characterised. Use of the complete genomic sequences of Oryza sativa L. and A. thaliana, as well as the partially assembled genomic data of Medicago truncatula L. and Brassica spp., allowed us to identify a new family of ATP-dependent DNA ligases that are found only in the Viridiplantae kingdom. An in-depth phylogenetic analysis of protein sequences showed that this family composes a distinct clade, which shares a last universal common ancestor with DNA ligases I. In silico sequence studies indicate that these proteins have distinct physico-chemical properties when compared with those of animal and fungal DNA ligases. Moreover, hydrophobic cluster analysis and 3-dimensional modelling allowed us to map two conserved domains within these DNA ligases I-like proteins. Additional data of microsynteny analysis indicate that these DNA ligases I-like genes are linked to the S and SLL2 loci of Brassica spp. and A. thaliana, respectively. Combining the results of all analyses, we propose the creation of the DNA ligases VI (LIG6) family, which is composed by plant-specific DNA ligases.
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Affiliation(s)
- Diego Bonatto
- Departamento de Biofísica/Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves 9500, 91507-970 Porto Alegre, RS, Brazil
| | - Martin Brendel
- Departamento de Biofísica/Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves 9500, 91507-970 Porto Alegre, RS, Brazil
| | - João Antonio Pêgas Henriques
- Departamento de Biofísica/Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves 9500, 91507-970 Porto Alegre, RS, Brazil
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57
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Bonatto D, Revers LF, Brendel M, Henriques JAP. The eukaryotic Pso2/Snm1/Artemis proteins and their function as genomic and cellular caretakers. Braz J Med Biol Res 2005; 38:321-34. [PMID: 15761611 DOI: 10.1590/s0100-879x2005000300002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA double-strand breaks (DSBs) represent a major threat to the genomic stability of eukaryotic cells. DNA repair mechanisms such as non-homologous end joining (NHEJ) are responsible for the maintenance of eukaryotic genomes. Dysfunction of one or more of the many protein complexes that function in NHEJ can lead to sensitivity to DNA damaging agents, apoptosis, genomic instability, and severe combined immunodeficiency. One protein, Pso2p, was shown to participate in the repair of DSBs induced by DNA inter-strand cross-linking (ICL) agents such as cisplatin, nitrogen mustard or photo-activated bi-functional psoralens. The molecular function of Pso2p in DNA repair is unknown, but yeast and mammalian cell line mutants for PSO2 show the same cellular responses as strains with defects in NHEJ, e.g., sensitivity to ICLs and apoptosis. The Pso2p human homologue Artemis participates in V(D)J recombination. Mutations in Artemis induce a variety of immunological deficiencies, a predisposition to lymphomas, and an increase in chromosomal aberrations. In order to better understand the role of Pso2p in the repair of DSBs generated as repair intermediates of ICLs, an in silico approach was used to characterize the catalytic domain of Pso2p, which led to identification of novel Pso2p homologues in other organisms. Moreover, we found the catalytic core of Pso2p fused to different domains. In plants, a specific ATP-dependent DNA ligase I contains the catalytic core of Pso2p, constituting a new DNA ligase family, which was named LIG6. The possible functions of Pso2p/Artemis/Lig6p in NHEJ and V(D)J recombination and in other cellular metabolic reactions are discussed.
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Affiliation(s)
- D Bonatto
- Departamento de Biofísica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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58
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Windels P, De Buck S, Van Bockstaele E, De Loose M, Depicker A. T-DNA integration in Arabidopsis chromosomes. Presence and origin of filler DNA sequences. PLANT PHYSIOLOGY 2003; 133:2061-8. [PMID: 14645727 PMCID: PMC300757 DOI: 10.1104/pp.103.027532] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2003] [Revised: 07/20/2003] [Accepted: 08/21/2003] [Indexed: 05/20/2023]
Abstract
To investigate the relationship between T-DNA integration and double-stranded break (DSB) repair in Arabidopsis, we studied 67 T-DNA/plant DNA junctions and 13 T-DNA/T-DNA junctions derived from transgenic plants. Three different types of T-DNA-associated joining could be distinguished. A minority of T-DNA/plant DNA junctions were joined by a simple ligation-like mechanism, resulting in a junction without microhomology or filler DNA insertions. For about one-half of all analyzed junctions, joining of the two ends occurred without insertion of filler sequences. For these junctions, microhomology was strikingly combined with deletions of the T-DNA ends. For the remaining plant DNA/T-DNA junctions, up to 51-bp-long filler sequences were present between plant DNA and T-DNA contiguous sequences. These filler segments are built from several short sequence motifs, identical to sequence blocks that occur in the T-DNA ends and/or the plant DNA close to the integration site. Mutual microhomologies among the sequence motifs that constitute a filler segment were frequently observed. When T-DNA integration and DSB repair were compared, the most conspicuous difference was the frequency and the structural organization of the filler insertions. In Arabidopsis, no filler insertions were found at DSB repair junctions. In maize (Zea mays) and tobacco (Nicotiana tabacum), DSB repair-associated filler was normally composed of simple, uninterrupted sequence blocks. Thus, although DSB repair and T-DNA integration are probably closely related, both mechanisms have some exclusive and specific characteristics.
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Affiliation(s)
- Pieter Windels
- Department of Plant Genetics and Breeding, Center of Agricultural Research-Gent, Caritasstraat 21, B-9090 Melle, Belgium
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59
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Gallego ME, Bleuyard JY, Daoudal-Cotterell S, Jallut N, White CI. Ku80 plays a role in non-homologous recombination but is not required for T-DNA integration in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:557-565. [PMID: 12940949 DOI: 10.1046/j.1365-313x.2003.01827.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chromosomal breaks are repaired by homologous recombination (HR) or non-homologous end joining (NHEJ) mechanisms. The Ku70/Ku80 heterodimer binds DNA ends and plays roles in NHEJ and telomere maintenance in organisms ranging from yeast to humans. We have previously identified a ku80 mutant of the model plant Arabidopsis thaliana and shown the role of Ku80 in telomere homeostasis in plant cells. We show here that this mutant is hypersensitive to the DNA-damaging agent methyl methane sulphonate and has a reduced capacity to carry out NHEJ recombination. To understand the interplay between HR and NHEJ in plants, we measured HR in the absence of Ku80. We find that the frequency of intrachromosomal HR is not affected by the absence of Ku80. Previous work has clearly implicated the Ku heterodimer in Agrobacterium-mediated T-DNA transformation of yeast. Surprisingly, ku80 mutant plants show no defect in the efficiency of T-DNA transformation of plants with Agrobacterium, showing that an alternative pathway must exist in plants.
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Affiliation(s)
- M E Gallego
- CNRS UMR 6547, Université Blaise Pascal, 24 avenue des Landais, 63177 Aubière, France
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60
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Chen MH, Citovsky V. Systemic movement of a tobamovirus requires host cell pectin methylesterase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:771-86. [PMID: 12887589 DOI: 10.1046/j.1365-313x.2003.01847.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Systemic movement of plant viruses through the host vasculature, one of the central events of the infection process, is essential for maximal viral accumulation and development of disease symptoms. The host plant proteins involved in this transport, however, remain unknown. Here, we examined whether or not pectin methylesterase (PME), one of the few cellular proteins known to be involved in local, cell-to-cell movement of tobacco mosaic virus (TMV), is also required for the systemic spread of viral infection through the plant vascular system. In a reverse genetics approach, PME levels were reduced in tobacco plants using antisense suppression. The resulting PME antisense plants displayed a significant degree of PME suppression in their vascular tissues but retained the wild-type pattern of phloem loading and unloading of a fluorescent solute. Systemic transport of TMV in these plants, however, was substantially delayed as compared to the wild-type tobacco, suggesting a role for PME in TMV systemic infection. Our analysis of virus distribution in the PME antisense plants suggested that TMV systemic movement may be a polar process in which the virions enter and exit the vascular system by two different mechanisms, and it is the viral exit out of the vascular system that involves PME.
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Affiliation(s)
- Min-Huei Chen
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
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61
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Namekawa S, Ichijima Y, Hamada F, Kasai N, Iwabata K, Nara T, Teraoka H, Sugawara F, Sakaguchi K. DNA ligase IV from a basidiomycete, Coprinus cinereus, and its expression during meiosis. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2119-2128. [PMID: 12904551 DOI: 10.1099/mic.0.26311-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA ligase IV is thought to be involved in DNA double-strand break repair and DNA non-homologous end-joining pathways, but these mechanisms are still unclear. To investigate the roles of DNA ligase IV from a biologically functional viewpoint, the authors studied its relationship to meiosis in a basidiomycete, Coprinus cinereus, which shows a highly synchronous meiotic cell cycle. The C. cinereus cDNA homologue of DNA ligase IV (CcLIG4) was successfully cloned. The 3.2 kb clone including the ORF encoded a predicted product of 1025 amino acid residues with a molecular mass of 117 kDa. A specific inserted sequence composed of 95 amino acids rich in aspartic acid and glutamic acid could be detected between tandem BRCT domains. The inserted sequence had no sequence identity with other eukaryotic counterparts of DNA ligase IV or with another aspartic acid and glutamic acid rich sequence inserted in C. cinereus proliferating cell nuclear antigen (CcPCNA), although the length and the percentages of aspartic and glutamic acids were similar. In addition, the recombinant CcLIG4 protein not only showed ATP-dependent ligase activity, but also used (dT)(16)/poly(dA) and (dT)(16)/poly(rA) as substrates, and had double-strand ligation activity, like human DNA ligase IV. Northern hybridization analysis and in situ hybridization indicated that CcLIG4 was expressed not only at the pre-meiotic S phase but also at meiotic prophase I. Intense signals were observed in leptotene and zygotene. Based on these observations, the possible role(s) of C. cinereus DNA ligase IV during meiosis are discussed.
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Affiliation(s)
- Satoshi Namekawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan
| | - Yosuke Ichijima
- Department of Pathological Biochemistry, Medical Research Institute, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Fumika Hamada
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan
| | - Nobuyuki Kasai
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan
| | - Kazuki Iwabata
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan
| | - Takayuki Nara
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan
| | - Hirobumi Teraoka
- Department of Pathological Biochemistry, Medical Research Institute, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Fumio Sugawara
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan
| | - Kengo Sakaguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan
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62
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van Attikum H, Bundock P, Overmeer RM, Lee LY, Gelvin SB, Hooykaas PJJ. The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but not for the integration of Agrobacterium T-DNA. Nucleic Acids Res 2003; 31:4247-55. [PMID: 12853643 PMCID: PMC165973 DOI: 10.1093/nar/gkg458] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2002] [Revised: 02/06/2003] [Accepted: 05/13/2003] [Indexed: 11/13/2022] Open
Abstract
The joining of breaks in the chromosomal DNA backbone by ligases in processes of replication, recombination and repair plays a crucial role in the maintenance of genomic stability. Four ATP-dependent ligases, designated DNA ligases I-IV, have been identified in higher eukaryotes, and each one has distinct functions. In mammals and yeast, DNA ligase IV is exclusively involved in the repair of DNA double-strand breaks by non-homologous end joining. Recently, an Arabidopsis thaliana orthologue of the yeast and mammalian DNA ligase IV gene was found and termed AtLIG4. Here we describe the isolation and functional characterisation of a plant line with a T-DNA insertion in the AtLIG4 gene. Plants homozygous for the T-DNA insertion did not display any growth or developmental defects and were fertile. However, mutant seedlings were hypersensitive to the DNA-damaging agents methyl methanesulfonate and X-rays, demonstrating that AtLIG4 is required for the repair of DNA damage. Recently, we showed that a yeast lig4 mutant is deficient in Agrobacterium T-DNA integration. However, using tumorigenesis and germline transformation assays, we found that the plant AtLIG4 mutant is not impaired in T-DNA integration. Thus, in contrast to yeast, DNA ligase IV is not required for T-DNA integration in plants.
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Affiliation(s)
- Haico van Attikum
- Institute of Biology, Leiden University, Clusius Laboratory, Wassenaarseweg 64, 2333 AL, Leiden, The Netherlands
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63
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Puchta H. Towards the ideal GMP: homologous recombination and marker gene excision. JOURNAL OF PLANT PHYSIOLOGY 2003; 160:743-754. [PMID: 12940543 DOI: 10.1078/0176-1617-01027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A mayor aim of biotechnology is the establishment of techniques for the precise manipulation of plant genomes. Two major efforts have been undertaken over the last dozen years, one to set up techniques for site-specific alteration of the plant genome via homologous recombination ("gene targeting") and the other for the removal of selectable marker genes from transgenic plants. Unfortunately, despite multiple promising approaches that will be shortly described in this review no feasible gene targeting technique has been developed till now for crop plants. In contrast, several alternative procedures have been established successfully to remove selectable markers from plant genomes. Intriguingly besides techniques relying on transposons and site-specific recombinases, recent results indicate that homologous recombination might be a valuable alternative for the excision of marker genes.
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Affiliation(s)
- Holger Puchta
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany.
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64
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Friesner J, Britt AB. Ku80- and DNA ligase IV-deficient plants are sensitive to ionizing radiation and defective in T-DNA integration. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:427-440. [PMID: 12753583 DOI: 10.1046/j.1365-313x.2003.01738.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Double-strand break (DSB) repair pathways catalyze the rejoining of broken chromosomes and the integration of transforming DNAs. These processes have been well characterized in bacteria, fungi, and animals. Plants are generally thought primarily to utilize a non-homologous end joining (NHEJ) pathway to repair DSBs and integrate transgenes, as transforming DNAs with large tracts of homology to the chromosome are integrated at random. In order to test the hypothesis that NHEJ is an important pathway for the repair of DSBs in plants, we isolated T-DNA insertion mutations in the Arabidopsis homologs of the Ku80 and DNA ligase IV genes, required for the initiation and completion, respectively, of NHEJ. Both mutants were hypersensitive to the cytostatic effects of gamma radiation, suggesting that NHEJ is indeed a critical pathway for the repair of DSBs. T-DNA insertion rates were also decreased in the mutants, indicating that Ku80 and DNA ligase IV play an important role in either the mechanism or the regulation of T-DNA integration in Arabidopsis.
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65
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Lafarge S, Montané MH. Characterization of Arabidopsis thaliana ortholog of the human breast cancer susceptibility gene 1: AtBRCA1, strongly induced by gamma rays. Nucleic Acids Res 2003; 31:1148-55. [PMID: 12582233 PMCID: PMC150221 DOI: 10.1093/nar/gkg202] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
hBRCA1 is involved in 20-45% of inherited breast cancer cases and is implicated in many mechanisms involved in response to DNA damage. To date, BRCA1 orthologs have been characterized in vertebrate genomes only. We have identified the ortholog of BRCA1 in Arabidopsis thaliana. AtBRCA1 is a 5.5 kb part of the locus At4g21070. The corresponding mRNA of 3.5 kb is composed of 14 exons and encodes a 941 amino acid protein (104 kDa). AtBRCA1, which has one N-terminal RING finger, two C-terminal BRCT and the p300/CBP interacting domain, shows a high similarity to hBRCA1 in these motifs and has the same characteristic molecular organization. We have also identified a putative ortholog in rice (OsBRCA1). With 941 and 968 amino acids, respectively, AtBRCA1 and OsBRCA1 are the shortest members of the BRCA1 family, and may represent a plant specificity. AtBRCA1 is expressed ubiquitously in plant tissues, at levels depending on organ type, with highest levels in flower buds and exponentially growing cell cultures. Increase of mRNA levels in all plant tissues 1 h after irradiation with the highest induction level of approximately 150 times for a 100 Gy dose is consistent with a putative role of AtBRCA1 in DNA repair and in cell-cycle control.
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Affiliation(s)
- S Lafarge
- CEA Cadarache, DSV-DEVM, Laboratoire de Radiobiologie Végétale, Bat 185, F-13108 St Paul Lez Durance Cedex, France
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66
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Reiss B. Homologous recombination and gene targeting in plant cells. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 228:85-139. [PMID: 14667043 DOI: 10.1016/s0074-7696(03)28003-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gene targeting has become an indispensable tool for functional genomics in yeast and mouse; however, this tool is still missing in plants. This review discusses the gene targeting problem in plants in the context of general knowledge on recombination and gene targeting. An overview on the history of gene targeting is followed by a general introduction to genetic recombination of bacteria, yeast, and vertebrates. This abridged discussion serves as a guide to the following sections, which cover plant-specific aspects of recombination assay systems, the mechanism of recombination, plant recombination genes, the relationship of recombination to the environment, approaches to stimulate homologous recombination and gene targeting, and a description of two plant systems, the moss Physcomitrella patens and the chloroplast, that naturally have high efficiencies of gene targeting. The review concludes with a discussion of alternatives to gene targeting.
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Affiliation(s)
- Bernd Reiss
- Max-Planck-Institut für Zuechtungsforschung, Carl-von-Linne-Weg 10, D-50829 Köln, Germany
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67
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Garcia V, Bruchet H, Camescasse D, Granier F, Bouchez D, Tissier A. AtATM is essential for meiosis and the somatic response to DNA damage in plants. THE PLANT CELL 2003; 15:119-32. [PMID: 12509526 PMCID: PMC143473 DOI: 10.1105/tpc.006577] [Citation(s) in RCA: 211] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2002] [Accepted: 10/25/2002] [Indexed: 05/17/2023]
Abstract
In contrast to yeast or mammalian cells, little is known about the signaling responses to DNA damage in plants. We previously characterized AtATM, an Arabidopsis homolog of the human ATM gene, which is mutated in ataxia telangiectasia, a chromosome instability disorder. The Atm protein is a protein kinase whose activity is induced by DNA damage, particularly DNA double-strand breaks. The phosphorylation targets of Atm include proteins involved in DNA repair, cell cycle control, and apoptosis. Here, we describe the isolation and functional characterization of two Arabidopsis mutants carrying a T-DNA insertion in AtATM. Arabidopsis atm mutants are hypersensitive to gamma-radiation and methylmethane sulfonate but not to UV-B light. In correlation with the radiation sensitivity, atm mutants failed to induce the transcription of genes involved in the repair and/or detection of DNA breaks upon irradiation. In addition, atm mutants are partially sterile, and we show that this effect is attributable to abundant chromosomal fragmentation during meiosis. Interestingly, the transcription of DNA recombination genes during meiosis was not dependent on AtATM, and meiotic recombination occurred at the same rate as in wild-type plants, raising questions about the function of AtAtm during meiosis in plants. Our results demonstrate that AtATM plays a central role in the response to both stress-induced and developmentally programmed DNA damage.
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Affiliation(s)
- Valérie Garcia
- Laboratoire de Radiobiologie Végétale, Département d'Ecophysiologie Végétale et de Microbiologie, Commissariat à l'Energie Atomique, 13108 St. Paul-lez-Durance Cedex, France
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68
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Abstract
Broken chromosomal ends in somatic cells of higher plants frequently heal by the ligation of DNA ends to unrelated sequences or to sequences with micro-homologies. This pathway of DNA-strand-break repair is the bane of gene-targeting attempts in plants. However, there is a second somatic pathway of chromosome repair, which is driven by DNA-sequence homology. Observations from yeast, fly and plants of homologous-recombination mechanisms point towards new strategies of gene targeting in plants.
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Affiliation(s)
- Animesh Ray
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
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69
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Hays JB. Arabidopsis thaliana, a versatile model system for study of eukaryotic genome-maintenance functions. DNA Repair (Amst) 2002; 1:579-600. [PMID: 12509283 DOI: 10.1016/s1568-7864(02)00093-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The genome of the model plant Arabidopsis thaliana encodes many orthologs of human genome-maintenance proteins, and in several important cases plant DNA repair and mutation-antagonism functions resemble their mammalian counterparts more closely than do those of established microbial models. These orthologs, in conjunction with the powerful tools now available for work with Arabidopsis and the practical advantages of its small size and rapid life cycle, now make it an attractive model system for study of eukaryotic DNA repair and mutagenesis. Already, null mutations that inactivate proteins involved in repair of DNA double-strand breaks or in DNA translesion synthesis and are lethal in mice have proved to be tolerated by plants. This review compares in some detail the genome-maintenance activities encoded by plants, mammals and microbes, and describes important Arabidopsis tools and life cycle characteristics. It concludes with selected examples that illustrate Arabidopsis advantages and/or reveal new insights into genome-maintenance functions of general interest.
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Affiliation(s)
- John B Hays
- Department of Environmental and Molecular Toxicology, 1007 ALS Building, Oregon State University, Corvallis, OR 97331-7301, USA.
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70
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West CE, Waterworth WM, Story GW, Sunderland PA, Jiang Q, Bray CM. Disruption of the Arabidopsis AtKu80 gene demonstrates an essential role for AtKu80 protein in efficient repair of DNA double-strand breaks in vivo. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 31:517-528. [PMID: 12182708 DOI: 10.1046/j.1365-313x.2002.01370.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Double-strand breaks (DSBs) in DNA may occur spontaneously in the cell or be induced experimentally by gamma-irradiation, and represent one of the most serious threats to genomic integrity. Non-homologous end joining (NHEJ) rather than homologous recombination appears to be the major pathway for DSB repair in humans and plants, and it may also be the major route whereby T-DNA integrates into the plant genome during cell transformation. In yeast and mammals, the exposed ends of damaged DNA are bound with high affinity by a dimer of Ku70 and Ku80 proteins, which protects the ends from exonucleases and juxtaposes the two ends of the DSB, independent of sequence homology. Here we report the functional characterization of Ku70 and Ku80 from Arabidopsis thaliana, and demonstrate that AtKu80 and AtKu70 form a heterodimer with DNA binding activity that is specific for DNA ends. An atku80 knockout mutant shows hypersensitivity to the DNA-damaging agents menadione and bleomycin, consistent with a role for AtKu80 in the repair of DSBs in vivo in Arabidopsis.
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Affiliation(s)
- Christopher E West
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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71
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Riha K, Watson J, Parkey J, Shippen DE. Telomere length deregulation and enhanced sensitivity to genotoxic stress in Arabidopsis mutants deficient in Ku70. EMBO J 2002; 21:2819-26. [PMID: 12032094 PMCID: PMC126030 DOI: 10.1093/emboj/21.11.2819] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2001] [Revised: 04/04/2002] [Accepted: 04/04/2002] [Indexed: 02/05/2023] Open
Abstract
The Ku70/80 heterodimer is a critical component of the non-homologous end-joining (NHEJ) pathway and of the telomere cap in yeast and mammals. We report the molecular characterization of the KU70 and KU80 genes in Arabidopsis and describe the consequences of a Ku70 deficiency. Arabidopsis KU70/80 genes are ubiquitously expressed and their products form stable heterodimers in vitro. Plants harboring a T-DNA insertion in KU70 exhibit no growth or developmental defects under standard growth conditions. However, mutant seedlings are hypersensitive to gamma-irradiation-induced double-strand breaks. Unexpectedly, we found that mutants are hypersensitive to methyl methanosulfonate during seed germination, but lose this sensitivity in seedlings, implying that the requirement for NHEJ varies during plant development. Lack of Ku70 results in a dramatic deregulation of telomere length control, with mutant telomeres expanding to more than twice the size of wild type by the second generation. Furthermore, in contrast to the situation in mammals, chromosome fusions are not associated with a Ku deficiency in Arabidopsis. These findings imply that Ku may play a different role in capping plant and animal telomeres.
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Affiliation(s)
| | | | | | - Dorothy E. Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
Corresponding author e-mail:
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72
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Ma Y, Pannicke U, Schwarz K, Lieber MR. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 2002; 108:781-94. [PMID: 11955432 DOI: 10.1016/s0092-8674(02)00671-2] [Citation(s) in RCA: 781] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mutations in the Artemis protein in humans result in hypersensitivity to DNA double-strand break-inducing agents and absence of B and T lymphocytes (radiosensitive severe combined immune deficiency [RS-SCID]). Here, we report that Artemis forms a complex with the 469 kDa DNA-dependent protein kinase (DNA-PKcs) in the absence of DNA. The purified Artemis protein alone possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation, DNA-PKcs phosphorylates Artemis, and Artemis acquires endonucleolytic activity on 5' and 3' overhangs, as well as hairpins. Finally, the Artemis:DNA-PKcs complex can open hairpins generated by the RAG complex. Thus, DNA-PKcs regulates Artemis by both phosphorylation and complex formation to permit enzymatic activities that are critical for the hairpin-opening step of V(D)J recombination and for the 5' and 3' overhang processing in nonhomologous DNA end joining.
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Affiliation(s)
- Yunmei Ma
- Norris Comprehensive Cancer Center, Rm. 5428, Departments of Biochemistry & Molecular Biology, Pathology, Biological Sciences, and Molecular Microbiology & Immunology, 1441 Eastlake Avenue, Los Angeles, CA 90033, USA
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73
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Tamura K, Adachi Y, Chiba K, Oguchi K, Takahashi H. Identification of Ku70 and Ku80 homologues in Arabidopsis thaliana: evidence for a role in the repair of DNA double-strand breaks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 29:771-781. [PMID: 12148535 DOI: 10.1046/j.1365-313x.2002.01258.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In higher organisms such as mammals and plants, DNA double-strand breaks (DSBs) are repaired preferentially by non-homologous end joining (NHEJ) rather than by homologous recombination. The NHEJ pathway is mediated by Ku, a heterodimer of approximately 70 and 80 kDa subunits, which contributes to various aspects of the metabolism of DNA ends in eukaryotic cells. On the basis of their predicted sequence similarity to human Ku70 and Ku80, cDNAs encoding the first plant homologues of these proteins (AtKu70 and AtKu80, respectively) have now been isolated from Arabidopsis thaliana. AtKu70 and AtKu80 share 28.6 and 22.5% amino acid sequence identity with human Ku70 and Ku80, respectively. Yeast two-hybrid analysis demonstrated that AtKu70 and AtKu80 form a heterodimer, and electrophoretic mobility-shift assays revealed that this heterodimer binds to double-stranded telomeric and non-telomeric DNA sequences, but not to single-stranded DNA. The AtKu heterodimer also possesses single-stranded DNA-dependent ATPase and ATP-dependent DNA helicase activities. Reverse transcription and the polymerase chain reaction revealed that AtKu70 and AtKu80 genes are expressed widely but at low levels in plant tissues. The expression of these two genes in cultured cells was markedly increased in response to the generation of DSBs by bleomycin or methylmethane sulfonate. These results suggest that the evolutionarily conserved Ku70-Ku80 heterodimer functions in DSB repair by the NHEJ pathway in A. thaliana.
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Affiliation(s)
- Katsunori Tamura
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan
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74
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Abstract
After the elucidation of the sequence of the yeast genome a major effort was started to elucidate the biological function of all open reading frames of this organisms by targeted gene replacement via homologous recombination. The establishment of the complete sequence of the genome of Arabidopsis thaliana would principally allow a similar approach. However, over the past dozen years all attempts to establish an efficient gene targeting technique in flowering plants were in the end not successful. In contrast, in Physcomitrella patens an efficient gene targeting procedure has been set up, making the moss a valuable model system for plant molecular biologists. But also for flowering plants recently several new approaches--some of them based on the availability of the genomic sequence of Arabidopsis--were initiated that might finally result on the set up of a general applicable technique. Beside the production of hyper-recombinogenic plants either via expression or suppression of specific gene functions or via undirected mutagenesis, the application of chimeric oligonucleotides might result in major progress.
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Affiliation(s)
- Holger Puchta
- Institut fur Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany.
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75
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Hartung F, Puchta H. Molecular characterization of homologues of both subunits A (SPO11) and B of the archaebacterial topoisomerase 6 in plants. Gene 2001; 271:81-6. [PMID: 11410368 DOI: 10.1016/s0378-1119(01)00496-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Spo11 protein is an eukaryotic homologue of the topoisomerase 6 subunit A from archaebacteria. In yeast Spo11p has been found to bind covalently to double-strand breaks (DSBs) during meiosis. Single homologues of the SPO11 gene exist in various eukaryotes, except plants. Previously, we found in the Arabidopsis thaliana genome two ancient paralogs, AtSPO11-1 and 2. Here we report on the molecular characterization of a third one, AtSPO11-3. This puzzling finding might be explained by the fact that we detected additionally--for the first time outside of the archaebacterial kingdom--a homologue of the subunit B of topoisomerase 6, AtTOP6B. Both AtSPO11-3 and AtTOP6B are abundantly expressed in Arabidopsis and EST comparisons indicate the presence of both genes in various plant species. Via two hybrid studies we could demonstrate that full length AtTop6B is able to interact with AtSpo11-2 and 3 but not with AtSpo11-1. Our data suggest that plants possess in contrast to other eukaryotes an additional archaebacterial kind of topoisomerase.
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Affiliation(s)
- F Hartung
- Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
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76
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Abstract
DNA ligases join breaks in the phosphodiester backbone of DNA molecules and are used in many essential reactions within the cell. All DNA ligases follow the same reaction mechanism, but they may use either ATP or NAD+ as a cofactor. All Bacteria (eubacteria) contain NAD+-dependent DNA ligases, and the uniqueness of these enzymes to Bacteria makes them an attractive target for novel antibiotics. In addition to their NAD+-dependent enzymes, some Bacteria contain genes for putative ATP-dependent DNA ligases. The requirement for these different isozymes in Bacteria is unknown, but may be related to their utilization in different aspects of DNA metabolism. The putative ATP-dependent DNA ligases found in Bacteria are most closely related to proteins from Archaea and viruses. Phylogenetic analysis suggests that all NAD+-dependent DNA ligases are closely related, but the ATP-dependent enzymes have been acquired by Bacterial genomes on a number of separate occasions.
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Affiliation(s)
- A Wilkinson
- Molecular Biology Sector, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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77
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Abstract
Meiosis is pivotal in the life history of plants. In addition to providing an opportunity for genetic reassortment, it marks the transition from diploid sporophyte to haploid gametophyte. Recent molecular data suggest that, like animals, plants possess a common set of genes (also conserved in eukaryotic microorganisms) responsible for meiotic recombination and chromosome segregation. However, unlike animals, plant meiocytes do not differentiate from a pool of primordial germ cells, but rather arise de novo from a germline formed from sub-epidermal cells in the anthers and ovules. Mutants defective in the specification of these reproductive cell lines and disrupted in different aspects of the meiotic process are beginning to reveal many features unique to plant meiosis.
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Affiliation(s)
- A M Bhatt
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK OX1 3RB.
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