1
|
Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B. De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing. THE PLANT CELL 2017; 29:2336-2348. [PMID: 29025960 PMCID: PMC5774570 DOI: 10.1105/tpc.17.00521] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/15/2017] [Accepted: 10/11/2017] [Indexed: 05/19/2023]
Abstract
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
Collapse
Affiliation(s)
- Maximilian H-W Schmidt
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Alexander Vogel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Alisandra K Denton
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Benjamin Istace
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope, 91057 Evry, France
| | - Alexandra Wormit
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | | | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Janina Maß
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Christian Pfaff
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Ulrich Schurr
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Roger Chetelat
- C.M. Rick Tomato Genetics Resource Center, Department of Plant Sciences, University of California, Davis, California 95616
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope, 91057 Evry, France
| | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dani Zamir
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Anthony M Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| |
Collapse
|
2
|
Wan C, Li C, Ma X, Wang Y, Sun C, Huang R, Zhong P, Gao Z, Chen D, Xu Z, Zhu J, Gao X, Wang P, Deng X. GRY79 encoding a putative metallo-β-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. PLANT CELL REPORTS 2015; 34:1353-1363. [PMID: 25903544 DOI: 10.1007/s00299-015-1792-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/12/2015] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
The green - revertible yellow79 mutant resulting from a single-base mutation suggested that the GRY79 gene encoding a putative metallo-β-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. Functional studies of metallo-β-lactamases and trihelix transcription factors in higher plants remain very sparse. In this study, we isolated the green-revertible yellow79 (gry79) mutant in rice. The mutant developed yellow-green leaves before the three-leaf stage but recovered to normal green at the sixth-leaf stage. Meanwhile, the mutant exhibited reduced level of chlorophylls and arrested development of chloroplasts in the yellow leaves. Genetic analysis suggested that the mutant phenotype was controlled by a single recessive nuclear gene on rice chromosome 2. Map-based cloning revealed that the candidate gene was Os02g33610 encoding a putative metallo-β-lactamase-trihelix chimera. In the gry79 mutant, a single-base mutation occurred in coding region of the gene, resulting in an amino acid change in the encoded protein. Furthermore, the mutant phenotype was rescued by transformation with the wild-type gene. Therefore, we have confirmed that the gry79 mutant phenotype resulted from a single-base mutation in GRY79 (Os02g33610) gene, suggesting that the gene encoding a putative metallo-β-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. In addition, we considered that the gry79 mutant gene could be applicable as a leaf-color marker gene for efficient identification and elimination of false hybrids in commercial hybrid rice production.
Collapse
Affiliation(s)
- Chunmei Wan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
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.
Collapse
|
4
|
Munari FM, Guecheva TN, Bonatto D, Henriques JAP. New features on Pso2 protein family in DNA interstrand cross-link repair and in the maintenance of genomic integrity in Saccharomyces cerevisiae. Fungal Genet Biol 2013; 60:122-32. [PMID: 24076078 DOI: 10.1016/j.fgb.2013.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/11/2013] [Accepted: 09/15/2013] [Indexed: 11/27/2022]
Abstract
Pso2 protein, a member of the highly conserved metallo-β-lactamase (MBL) super family of nucleases, plays a central role in interstrand crosslink repair (ICL) in yeast. Pso2 protein is the founder member of a distinct group within the MBL superfamily, called β-CASP family. Three mammalian orthologs of this protein that act on DNA were identified: SNM1A, SNM1B/Apollo and SNM1C/Artemis. Yeast Pso2 and all three mammalian orthologs proteins have been shown to possess nuclease activity. Besides Pso2, ICL repair involves proteins of several DNA repair pathways. Over the last years, new homologs for human proteins have been identified in yeast. In this review, we will focus on studies clarifying the function of Pso2 protein during ICL repair in yeast, emphasizing the contribution of Brazilian research groups in this topic. New sub-pathways in the mechanisms of ICL repair, such as recently identified conserved Fanconi Anemia pathway in yeast as well as a contribution of non-homologous end joining are discussed.
Collapse
Affiliation(s)
- Fernanda Mosena Munari
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
| | | | | | | |
Collapse
|
5
|
Abstract
BACKGROUND Buffalograss [Buchloë dactyloides (Nutt.) Engel. syn. Bouteloua dactyloides (Nutt.) Columbus] is a United States native turfgrass species that requires less irrigation, fungicides and pesticides compared to more commonly used turfgrass species. In areas where water is limited, interest in this grass species for lawns is increasing. While several buffalograss cultivars have been developed through buffalograss breeding, the timeframe for new cultivar development is long and is limited by a lack of useful genetic resources. Two high throughput next-generation sequencing techniques were used to increase the genomic resources available for buffalograss. RESULTS Total RNA was extracted and purified from leaf samples of two buffalograss cultivars. '378' and 'Prestige' cDNA libraries were subjected to high throughput sequencing on the Illumina GA and Roche 454 Titanium FLX sequencing platforms. The 454 platform (3 samples) produced 1,300,885 reads and the Illumina platform (12 samples) generated approximately 332 million reads. The multiple k-mer technique for de novo assembly using Velvet and Oases was applied. A total of 121,288 contigs were assembled that were similar to previously reported Ensembl commelinid sequences. Original Illumina reads were also mapped to the high quality assembly to estimate expression levels of buffalograss transcripts. There were a total of 325 differentially expressed genes between the two buffalograss cultivars. A glycosyl transferase, serine threonine kinase, and nb-arc domain containing transcripts were among those differentially expressed between the two cultivars. These genes have been previously implicated in defense response pathways and may in part explain some of the performance differences between 'Prestige' and '378'. CONCLUSIONS To date, this is the first high throughput sequencing experiment conducted on buffalograss. In total, 121,288 high quality transcripts were assembled, significantly expanding the limited genetic resources available for buffalograss genetic studies. Additionally, 325 differentially expressed sequences were identified which may contribute to performance or morphological differences between 'Prestige' and '378' buffalograss cultivars.
Collapse
|
6
|
Chang CW, Couñago RLM, Williams SJ, Bodén M, Kobe B. Crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals. THE PLANT CELL 2012; 24:5074-88. [PMID: 23250448 PMCID: PMC3556976 DOI: 10.1105/tpc.112.104422] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/22/2012] [Accepted: 11/26/2012] [Indexed: 05/22/2023]
Abstract
In the classical nucleocytoplasmic import pathway, nuclear localization signals (NLSs) in cargo proteins are recognized by the import receptor importin-α. Importin-α has two separate NLS binding sites (the major and the minor site), both of which recognize positively charged amino acid clusters in NLSs. Little is known about the molecular basis of the unique features of the classical nuclear import pathway in plants. We determined the crystal structure of rice (Oryza sativa) importin-α1a at 2-Å resolution. The structure reveals that the autoinhibitory mechanism mediated by the importin-β binding domain of importin-α operates in plants, with NLS-mimicking sequences binding to both minor and major NLS binding sites. Consistent with yeast and mammalian proteins, rice importin-α binds the prototypical NLS from simian virus 40 large T-antigen preferentially at the major NLS binding site. We show that two NLSs, previously described as plant specific, bind to and are functional with plant, mammalian, and yeast importin-α proteins but interact with rice importin-α more strongly. The crystal structures of their complexes with rice importin-α show that they bind to the minor NLS binding site. By contrast, the crystal structures of their complexes with mouse (Mus musculus) importin-α show preferential binding to the major NLS binding site. Our results reveal the molecular basis of a number of features of the classical nuclear transport pathway specific to plants.
Collapse
Affiliation(s)
- Chiung-Wen Chang
- School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane Qld 4072, Australia
| | - Rafael Lemos Miguez Couñago
- School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane Qld 4072, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane Qld 4072, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia
- School of Information Technology and Electrical Engineering, University of Queensland, Brisbane Qld 4072, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane Qld 4072, Australia
- Address correspondence to
| |
Collapse
|
7
|
Charbonnel C, Gallego ME, White CI. Xrcc1-dependent and Ku-dependent DNA double-strand break repair kinetics in Arabidopsis plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:280-90. [PMID: 21070408 DOI: 10.1111/j.1365-313x.2010.04331.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Double-strand breakage (DSB) of DNA involves loss of information on the two strands of the DNA fibre and thus cannot be repaired by simple copying of the complementary strand which is possible with single-strand DNA damage. Homologous recombination (HR) can precisely repair DSB using another copy of the genome as template and non-homologous recombination (NHR) permits repair of DSB with little or no dependence on DNA sequence homology. In addition to the well-characterised Ku-dependent non-homologous end-joining (NHEJ) pathway, much recent attention has been focused on Ku-independent NHR. The complex interrelationships and regulation of NHR pathways remain poorly understood, even more so in the case of plants, and we present here an analysis of Ku-dependent and Ku-independent repair of DSB in Arabidopsis thaliana. We have characterised an Arabidopsis xrcc1 mutant and developed quantitative analysis of the kinetics of appearance and loss of γ-H2AX foci as a tool to measure DSB repair in dividing root tip cells of γ-irradiated plants in vivo. This approach has permitted determination of DSB repair kinetics in planta following a short pulse of γ-irradiation, establishing the existence of a Ku-independent, Xrcc1-dependent DSB repair pathway. Furthermore, our data show a role for Ku80 during the first minutes post-irradiation and that Xrcc1 also plays such a role, but only in the absence of Ku. The importance of Xrcc1 is, however, clearly visible at later times in the presence of Ku, showing that alternative end-joining plays an important role in DSB repair even in the presence of active NHEJ.
Collapse
Affiliation(s)
- Cyril Charbonnel
- Génétique, Reproduction et Développement, UMR CNRS 6247 - Clermont Université- INSERM U931, Université Blaise Pascal, UFR Sciences et Technologies, 24 Avenue des Landais, Aubière Cedex, France
| | | | | |
Collapse
|
8
|
Waterworth WM, Masnavi G, Bhardwaj RM, Jiang Q, Bray CM, West CE. A plant DNA ligase is an important determinant of seed longevity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:848-60. [PMID: 20584150 DOI: 10.1111/j.1365-313x.2010.04285.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA repair is important for maintaining genome integrity. In plants, DNA damage accumulated in the embryo of seeds is repaired early in imbibition, and is important for germination performance and seed longevity. An essential step in most repair pathways is the DNA ligase-mediated rejoining of single- and double-strand breaks. Eukaryotes possess multiple DNA ligase enzymes, each having distinct roles in cellular metabolism. Here, we report the characterization of DNA LIGASE VI, which is only found in plant species. The primary structure of this ligase shows a unique N-terminal region that contains a β-CASP motif, which is found in a number of repair proteins, including the DNA double-strand break (DSB) repair factor Artemis. Phenotypic analysis revealed a delay in the germination of atlig6 mutants compared with wild-type lines, and this delay becomes markedly exacerbated in the presence of the genotoxin menadione. Arabidopsis atlig6 and atlig6 atlig4 mutants display significant hypersensitivity to controlled seed ageing, resulting in delayed germination and reduced seed viability relative to wild-type lines. In addition, atlig6 and atlig6 atlig4 mutants display increased sensitivity to low-temperature stress, resulting in delayed germination and reduced seedling vigour upon transfer to standard growth conditions. Seeds display a rapid transcriptional DNA DSB response, which is activated in the earliest stages of water imbibition, providing evidence for the accumulation of cytotoxic DSBs in the quiescent seed. These results implicate AtLIG6 and AtLIG4 as major determinants of Arabidopsis seed quality and longevity.
Collapse
|
9
|
Singh SK, Roy S, Choudhury SR, Sengupta DN. DNA repair and recombination in higher plants: insights from comparative genomics of Arabidopsis and rice. BMC Genomics 2010; 11:443. [PMID: 20646326 PMCID: PMC3091640 DOI: 10.1186/1471-2164-11-443] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 07/21/2010] [Indexed: 11/13/2022] Open
Abstract
Background The DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them. Results We identified genes potentially involved in DRR mechanisms in Arabidopsis and rice using similarity searches and conserved domain analysis against proteins known to be involved in DRR in human, yeast and E. coli. As expected, many of DRR genes are very similar to those found in other eukaryotes. Beside these eukaryotes specific genes, several prokaryotes specific genes were also found to be well conserved in plants. In Arabidopsis, several functionally important DRR gene duplications are present, which do not occur in rice. Among DRR proteins, we found that proteins belonging to the nucleotide excision repair pathway were relatively more conserved than proteins needed for the other DRR pathways. Sub-cellular localization studies of DRR gene suggests that these proteins are mostly reside in nucleus while gene drain in between nucleus and cell organelles were also found in some cases. Conclusions The similarities and dissimilarities in between plants and other organisms' DRR pathways are discussed. The observed differences broaden our knowledge about DRR in the plants world, and raises the potential question of whether differentiated functions have evolved in some cases. These results, altogether, provide a useful framework for further experimental studies in these organisms.
Collapse
Affiliation(s)
- Sanjay K Singh
- Department of Botany, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700 009, India.
| | | | | | | |
Collapse
|
10
|
Cattell E, Sengerová B, McHugh PJ. The SNM1/Pso2 family of ICL repair nucleases: from yeast to man. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:635-645. [PMID: 20175117 DOI: 10.1002/em.20556] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Efficient interstrand crosslink (ICL) repair in yeast depends on the Pso2/Snm1 protein. Pso2 is a member of the highly conserved metallo-beta-lactamase structural family of nucleases. Mammalian cells possess three SNM1/Pso2 related proteins, SNM1A, SNM1B/Apollo, and SNM1C/Artemis. Evidence that SNM1A and SNM1B contribute to ICL repair is mounting, whereas Artemis appears to primarily contribute to non-ICL repair pathways, particularly some double-strand break repair events. Yeast Pso2 and all three mammalian SNM1-family proteins have been shown to possess nuclease activity. Here, we review the biochemical, genetic, and cellular evidence for the SNM1 family as DNA repair factors, focusing on ICL repair.
Collapse
Affiliation(s)
- Emma Cattell
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | | | | |
Collapse
|
11
|
Repair and tolerance of oxidative DNA damage in plants. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2009; 681:169-179. [DOI: 10.1016/j.mrrev.2008.07.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 07/11/2008] [Accepted: 07/17/2008] [Indexed: 11/19/2022]
|
12
|
Gaut BS, Wright SI, Rizzon C, Dvorak J, Anderson LK. Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genet 2007; 8:77-84. [PMID: 17173059 DOI: 10.1038/nrg1970] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.
Collapse
Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA.
| | | | | | | | | |
Collapse
|
13
|
Reidt W, Wurz R, Wanieck K, Chu HH, Puchta H. A homologue of the breast cancer-associated gene BARD1 is involved in DNA repair in plants. EMBO J 2006; 25:4326-37. [PMID: 16957774 PMCID: PMC1570427 DOI: 10.1038/sj.emboj.7601313] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Accepted: 08/03/2006] [Indexed: 01/09/2023] Open
Abstract
hBRCA1 and hBARD1 are tumor suppressor proteins that are involved as heterodimer via ubiquitinylation in many cellular processes, such as DNA repair. Loss of BRCA1 or BARD1 results in early embryonic lethality and chromosomal instability. The Arabidopsis genome carries a BRCA1 homologue, and we were able to identify a BARD1 homologue. AtBRCA1 and the putative AtBARD1 protein are able to interact with each other as indicated by in vitro and in planta experiments. We have identified T-DNA insertion mutants for both genes, which show no visible phenotype under standard growth conditions and are fully fertile. Thus, in contrast to animals, both genes have no indispensable role during development and meiosis in plants. The two single as well as the double mutant are to a similar extent sensitive to mitomycin C, indicating an epistatic interaction in DNA crosslink repair. We could further demonstrate that in Arabidopsis BARD1 plays a prominent role in the regulation of homologous DNA repair in somatic cells.
Collapse
Affiliation(s)
- Wim Reidt
- Botanisches Institut II, Universität Karlsruhe, Karlsruhe, Germany
| | - Rebecca Wurz
- Botanisches Institut II, Universität Karlsruhe, Karlsruhe, Germany
| | - Kristina Wanieck
- Botanisches Institut II, Universität Karlsruhe, Karlsruhe, Germany
| | - Hoang Ha Chu
- Botanisches Institut II, Universität Karlsruhe, Karlsruhe, Germany
| | - Holger Puchta
- Botanisches Institut II, Universität Karlsruhe, Karlsruhe, Germany
| |
Collapse
|
14
|
Saotome A, Kimura S, Mori Y, Uchiyama Y, Morohashi K, Sakaguchi K. Characterization of four RecQ homologues from rice (Oryza sativa L. cv. Nipponbare). Biochem Biophys Res Commun 2006; 345:1283-91. [PMID: 16730655 DOI: 10.1016/j.bbrc.2006.04.134] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Accepted: 04/14/2006] [Indexed: 11/19/2022]
Abstract
The RecQ family of DNA helicases is conserved throughout the biological kingdoms. In this report, we have characterized four RecQ homologues clearly expressed in rice. OsRecQ1, OsRecQ886, and OsRecQsim expressions were strongly detected in meristematic tissues. Transcription of the OsRecQ homologues was differentially induced by several types of DNA-damaging agents. The expression of four OsRecQ homologues was induced by MMS and bleomycin. OsRecQ1 and OsRecQ886 were induced by H(2)O(2), and MitomycinC strongly induced the expression of OsRecQ1. Transient expression of OsRecQ/GFP fusion proteins demonstrated that OsRecQ2 and OsRecQ886 are found in nuclei, whereas OsRecQ1 and OsRecQsim are found in plastids. Neither OsRecQ1 nor OsRecQsim are induced by light. These results indicate that four of the RecQ homologues have different and specific functions in DNA repair pathways, and that OsRecQ1 and OsRecQsim may not involve in plastid differentiation but different aspects of a plastid-specific DNA repair system.
Collapse
Affiliation(s)
- Ai Saotome
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | | | | | | | | | | |
Collapse
|
15
|
Affiliation(s)
- Seisuke Kimura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda-shi, Chiba, Japan
| | | |
Collapse
|
16
|
Bonatto D, Brendel M, Henriques JAP. The eukaryotic Pso2p/Snm1p family revisited: in silico analyses of Pso2p A, B and Plasmodium groups. Comput Biol Chem 2005; 29:420-33. [PMID: 16290064 DOI: 10.1016/j.compbiolchem.2005.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 09/24/2005] [Indexed: 11/28/2022]
Abstract
The eukaryotic family of Pso2/Snm1 exo/endonuclease proteins has important functions in repair of DNA damages induced by chemical interstrand cross-linking agents and ionizing radiation. These exo/endonucleases are also necessary for V(D)J recombination and genomic caretaking. However, despite the growing biochemical data about this family, little is known about the number of orthologous/paralogous Pso2p/Snm1p sequences in eukaryotes and how they are phylogenetically organized. In this work we have characterized new Pso2p/Snm1p sequences from the finished and unfinished eukaryotic genomes and performed an in-depth phylogenetic analysis. The results indicate that four phylogenetically related groups compose the Pso2p/Snm1p family: (i) the Artemis/Artemis-like group, (ii) the Pso2p A group, (iii) the Pso2p B group and (iv) the Pso2p Plasmodium group. Using the available biochemical and genomic information about Pso2p/Snm1p family, we concentrate our research in the study of Pso2p A, B and Plasmodium groups. The phylogenetic results showed that A and B groups can be organized in specific subgroups with different functions in DNA metabolism. Moreover, we subjected selected Pso2p A, B and Plasmodium proteins to hydrophobic cluster analysis (HCA) in order to map and to compare conserved regions within these sequences. Four conserved regions could be detected by HCA, which are distributed along the metallo-beta-lactamase and beta-CASP motifs. Interestingly, both Pso2p A and B proteins are structurally similar, while Pso2p Plasmodium proteins have a unique domain organization. The possible functions of A, B and Plasmodium groups are discussed.
Collapse
Affiliation(s)
- Diego Bonatto
- Departamento de Biofísica/Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, 91507-970 Porto Alegre, RS, Brazil
| | | | | |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Jean-Yves Bleuyard
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK.
| | | | | |
Collapse
|
18
|
Bonatto D, Brendel M, Henriques JAP. In silico Identification and Analysis of New Artemis/Artemis-like Sequences from Fungal and Metazoan Species. Protein J 2005; 24:399-411. [PMID: 16323046 DOI: 10.1007/s10930-005-7594-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Indexed: 02/01/2023]
Abstract
The Artemis Group comprises mammalian proteins with important functions in the repair of ionizing radiation-induced DNA double-strand breaks and in the cleavage of DNA hairpin extremities generated during V(D)J recombination. Little is known about the presence of Artemis/Artemis-like proteins in non-mammalian species. We have characterized new Artemis/Artemis-like sequences from the genomes of some fungi and from non-mammalian metazoan species. An in-depth phylogenetic analysis of these new Artemis/Artemis-like sequences showed that they form a distinct clade within the Pso2p/Snm1p A and B Groups. Hydrophobic cluster analysis and three-dimensional modeling allowed to map and to compare conserved regions in these Artemis/Artemis-like proteins. The results indicate that Artemis probably belongs to an ancient DNA recombination mechanism that diversified with the evolution of multi-cellular eukaryotic lineage.
Collapse
Affiliation(s)
- Diego Bonatto
- Departamento de Biofísica/Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91507-970, Porto Alegre, RS, Brazil
| | | | | |
Collapse
|
19
|
Barber LJ, Ward TA, Hartley JA, McHugh PJ. DNA interstrand cross-link repair in the Saccharomyces cerevisiae cell cycle: overlapping roles for PSO2 (SNM1) with MutS factors and EXO1 during S phase. Mol Cell Biol 2005; 25:2297-309. [PMID: 15743825 PMCID: PMC1061624 DOI: 10.1128/mcb.25.6.2297-2309.2005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pso2/Snm1 is a member of the beta-CASP metallo-beta-lactamase family of proteins that include the V(D)J recombination factor Artemis. Saccharomyces cerevisiae pso2 mutants are specifically sensitive to agents that induce DNA interstrand cross-links (ICLs). Here we establish a novel overlapping function for PSO2 with MutS mismatch repair factors and the 5'-3' exonuclease Exo1 in the repair of DNA ICLs, which is confined to S phase. Our data demonstrate a requirement for NER and Pso2, or Exo1 and MutS factors, in the processing of ICLs, and this is required prior to the repair of ICL-induced DNA double-strand breaks (DSBs) that form during replication. Using a chromosomally integrated inverted-repeat substrate, we also show that loss of both pso2 and exo1/msh2 reduces spontaneous homologous recombination rates. Therefore, PSO2, EXO1, and MSH2 also appear to have overlapping roles in the processing of some forms of endogenous DNA damage that occur at an irreversibly collapsed replication fork. Significantly, our analysis of ICL repair in cells synchronized for each cell cycle phase has revealed that homologous recombination does not play a major role in the direct repair of ICLs, even in G2, when a suitable template is readily available. Rather, we propose that recombination is primarily involved in the repair of DSBs that arise from the collapse of replication forks at ICLs. These findings have led to considerable clarification of the complex genetic relationship between various ICL repair pathways.
Collapse
Affiliation(s)
- Louise J Barber
- Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, Royal Free and University College Medical School, University College London, London
| | | | | | | |
Collapse
|
20
|
Kimura S, Saotome A, Uchiyama Y, Mori Y, Tahira Y, Sakaguchi K. The expression of the rice (Oryza sativa L.) homologue of Snm1 is induced by DNA damages. Biochem Biophys Res Commun 2005; 329:668-72. [PMID: 15737637 DOI: 10.1016/j.bbrc.2005.01.161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Indexed: 10/25/2022]
Abstract
We isolated and characterized the rice homologue of the DNA repair gene Snm1 (OsSnm1). The length of the cDNA was 1862bp; the open reading frame encoded a predicted product of 485 amino acid residues with a molecular mass of 53.2kDa. The OsSnm1 protein contained the conserved beta-lactamase domain in its internal region. OsSnm1 was expressed in all rice organs. The expression was induced by MMS, H(2)O(2), and mitomycin C, but not by UV. Transient expression of an OsSnm1/GFP fusion protein in onion epidermal cells revealed the localization of OsSnm1 to the nucleus. These results suggest that OsSnm1 is involved not only in the repair of DNA interstrand crosslinks, but also in various other DNA repair pathways.
Collapse
Affiliation(s)
- Seisuke Kimura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
| | | | | | | | | | | |
Collapse
|