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Olson CL, Wuttke DS. Guardians of the Genome: How the Single-Stranded DNA-Binding Proteins RPA and CST Facilitate Telomere Replication. Biomolecules 2024; 14:263. [PMID: 38540683 PMCID: PMC10968030 DOI: 10.3390/biom14030263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 04/26/2024] Open
Abstract
Telomeres act as the protective caps of eukaryotic linear chromosomes; thus, proper telomere maintenance is crucial for genome stability. Successful telomere replication is a cornerstone of telomere length regulation, but this process can be fraught due to the many intrinsic challenges telomeres pose to the replication machinery. In addition to the famous "end replication" problem due to the discontinuous nature of lagging strand synthesis, telomeres require various telomere-specific steps for maintaining the proper 3' overhang length. Bulk telomere replication also encounters its own difficulties as telomeres are prone to various forms of replication roadblocks. These roadblocks can result in an increase in replication stress that can cause replication forks to slow, stall, or become reversed. Ultimately, this leads to excess single-stranded DNA (ssDNA) that needs to be managed and protected for replication to continue and to prevent DNA damage and genome instability. RPA and CST are single-stranded DNA-binding protein complexes that play key roles in performing this task and help stabilize stalled forks for continued replication. The interplay between RPA and CST, their functions at telomeres during replication, and their specialized features for helping overcome replication stress at telomeres are the focus of this review.
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Affiliation(s)
- Conner L. Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
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2
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Hagihara M, Dohno C, Saito K, Sugimoto K, Hishinuma Y, Sohma Y, Shibata T, Nakatani K. Short Tandem Repeat Contractions during In Vitro DNA Synthesis by Repeat-binding Molecules. CHEM LETT 2021. [DOI: 10.1246/cl.210415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masaki Hagihara
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Chikara Dohno
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kaoru Saito
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Kazuhiro Sugimoto
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuta Hishinuma
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuri Sohma
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Tomonori Shibata
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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3
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Dohno C, Hagihara M, Binti Mohd Zaifuddin N, Nihei M, Saito K, Nakatani K. Small molecule-induced trinucleotide repeat contractions during in vitro DNA synthesis. Chem Commun (Camb) 2021; 57:3235-3238. [PMID: 33646236 DOI: 10.1039/d1cc00349f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrated that a synthetic ligand NA, which selectively binds to a 5'-CAG-3'/5'-CAG-3' triad, induced repeat contractions during DNA polymerase-mediated primer extension through the CAG repeat template. A thorough capillary electrophoresis and sequencing analysis revealed that the d(CAG)20 template gave shortened nascent strands mainly containing 3-6 CTG units in the presence of NA.
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Affiliation(s)
- Chikara Dohno
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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4
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Callahan BP, Ciulla DA, Wagner AG, Xu Z, Zhang X. Specificity Distorted: Chemical Induction of Biological Paracatalysis. Biochemistry 2020; 59:3517-3522. [PMID: 32931253 DOI: 10.1021/acs.biochem.0c00643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We define paracatalysis as the acceleration of a reaction that appears abnormal or nonphysiological. With the high specificity of enzymes, side reactivity of this kind is typically negligible. However, enzyme paracatalysis can be amplified to levels that are biologically significant through interactions with a special class of small molecule "antagonist", here termed a paracatalytic inducer. Compounds with this unusual mode of action tend to be natural products, identified by chance through phenotypic screens. In this Perspective, we suggest two general types of paracatalytic inducer. The first type promotes substrate ambiguity, where the enzyme's ground state selectivity is compromised, enabling the transformation of non-native substrates. The second type involves transition state ambiguity, where the paracatalytic inducer changes the enzyme's interactions with the activated substrate, giving rise to non-native bond making. Although they are unusual, small molecules that induce paracatalysis have established value as hypothesis-generating probes and a few substances, i.e., aspirin and the aminoglycosides, have proven to be translatable as medicines.
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Affiliation(s)
- Brian P Callahan
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Daniel A Ciulla
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Andrew G Wagner
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Zihan Xu
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Xiaoyu Zhang
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
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5
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Lobos-González L, Silva V, Araya M, Restovic F, Echenique J, Oliveira-Cruz L, Fitzpatrick C, Briones M, Villegas J, Villota C, Vidaurre S, Borgna V, Socias M, Valenzuela S, Lopez C, Socias T, Varas M, Díaz J, Burzio LO, Burzio VA. Targeting antisense mitochondrial ncRNAs inhibits murine melanoma tumor growth and metastasis through reduction in survival and invasion factors. Oncotarget 2018; 7:58331-58350. [PMID: 27507060 PMCID: PMC5295434 DOI: 10.18632/oncotarget.11110] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/19/2016] [Indexed: 01/23/2023] Open
Abstract
We reported that knockdown of the antisense noncoding mitochondrial RNAs (ASncmtRNAs) induces apoptotic death of several human tumor cell lines, but not normal cells, suggesting this approach for selective therapy against different types of cancer. In order to translate these results to a preclinical scenario, we characterized the murine noncoding mitochondrial RNAs (ncmtRNAs) and performed in vivo knockdown in syngeneic murine melanoma models. Mouse ncmtRNAs display structures similar to the human counterparts, including long double-stranded regions arising from the presence of inverted repeats. Knockdown of ASncmtRNAs with specific antisense oligonucleotides (ASO) reduces murine melanoma B16F10 cell proliferation and induces apoptosis in vitro through downregulation of pro-survival and metastasis markers, particularly survivin. For in vivo studies, subcutaneous B16F10 melanoma tumors in C57BL/6 mice were treated systemically with specific and control antisense oligonucleotides (ASO). For metastasis studies, tumors were resected, followed by systemic administration of ASOs and the presence of metastatic nodules in lungs and liver was assessed. Treatment with specific ASO inhibited tumor growth and metastasis after primary tumor resection. In a metastasis-only assay, mice inoculated intravenously with cells and treated with the same ASO displayed reduced number and size of melanoma nodules in the lungs, compared to controls. Our results suggest that ASncmtRNAs could be potent targets for melanoma therapy. To our knowledge, the ASncmtRNAs are the first potential non-nuclear targets for melanoma therapy.
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Affiliation(s)
- Lorena Lobos-González
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Facultad de Medicina, Universidad de Chile, Independencia, Santiago, Chile
| | - Verónica Silva
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile
| | - Mariela Araya
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile
| | - Franko Restovic
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Present address: Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Echenique
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile
| | - Luciana Oliveira-Cruz
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile
| | - Christopher Fitzpatrick
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Facultad de Ciencias Biológicas, Universidad Andrés Bello, República, Santiago, Chile
| | - Macarena Briones
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile
| | - Jaime Villegas
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Facultad de Ciencias Biológicas, Universidad Andrés Bello, República, Santiago, Chile
| | - Claudio Villota
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Facultad de Ciencias Biológicas, Universidad Andrés Bello, República, Santiago, Chile
| | - Soledad Vidaurre
- Andes Biotechnologies SpA, Santiago, Chile.,Facultad de Salud, Deporte y Recreación, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Vincenzo Borgna
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Servicio de Urología, Hospital Barros-Lucco-Trudeau, Santiago, Chile
| | | | | | - Constanza Lopez
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile
| | - Teresa Socias
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile
| | | | - Jorge Díaz
- Facultad de Medicina, Universidad de Chile, Independencia, Santiago, Chile
| | - Luis O Burzio
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Facultad de Ciencias Biológicas, Universidad Andrés Bello, República, Santiago, Chile
| | - Verónica A Burzio
- Andes Biotechnologies SpA, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Facultad de Ciencias Biológicas, Universidad Andrés Bello, República, Santiago, Chile
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6
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Yuan Z, Liu S, Zhou T, Tian C, Bao L, Dunham R, Liu Z. Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments. BMC Genomics 2018; 19:141. [PMID: 29439662 PMCID: PMC5811955 DOI: 10.1186/s12864-018-4516-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/31/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. RESULTS The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. CONCLUSIONS The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments. However, due to the restriction of the limited sequenced species, further analysis needs to be done to alleviate the phylogenetic biases.
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Affiliation(s)
- Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY 13244 USA
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7
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El Kafsi H, Loux V, Mariadassou M, Blin C, Chiapello H, Abraham AL, Maguin E, van de Guchte M. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Sci Rep 2017; 7:44331. [PMID: 28281695 PMCID: PMC5345009 DOI: 10.1038/srep44331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/07/2017] [Indexed: 12/29/2022] Open
Abstract
The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp.
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Affiliation(s)
- Hela El Kafsi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Camille Blin
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Hélène Chiapello
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Anne-Laure Abraham
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuelle Maguin
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Maarten van de Guchte
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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8
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Holder IT, Wagner S, Xiong P, Sinn M, Frickey T, Meyer A, Hartig JS. Intrastrand triplex DNA repeats in bacteria: a source of genomic instability. Nucleic Acids Res 2015; 43:10126-42. [PMID: 26450966 PMCID: PMC4666352 DOI: 10.1093/nar/gkv1017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
Repetitive nucleic acid sequences are often prone to form secondary structures distinct from B-DNA. Prominent examples of such structures are DNA triplexes. We observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. A systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the ITxF database available online at http://bioinformatics.uni-konstanz.de/utils/ITxF/. Next we investigated biophysical and biochemical properties of a particular G/C-rich triplex motif (TM) that occurs in many copies in more than 260 bacterial genomes by CD and nuclear magnetic resonance spectroscopy as well as in vivo footprinting techniques. A characterization of putative properties and functions of these unusually frequent nucleic acid motifs demonstrated that the occurrence of the TM is associated with a high degree of genomic instability. TM-containing genomic loci are significantly more rearranged among closely related Escherichia coli strains compared to control sites. In addition, we found very high frequencies of TM motifs in certain Enterobacteria and Cyanobacteria that were previously described as genetically highly diverse. In conclusion we link intrastrand triplex motifs with the induction of genomic instability. We speculate that the observed instability might be an adaptive feature of these genomes that creates variation for natural selection to act upon.
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Affiliation(s)
- Isabelle T Holder
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Stefanie Wagner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Peiwen Xiong
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Tancred Frickey
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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9
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Castillo-Lizardo M, Henneke G, Viguera E. Replication slippage of the thermophilic DNA polymerases B and D from the Euryarchaeota Pyrococcus abyssi. Front Microbiol 2014; 5:403. [PMID: 25177316 PMCID: PMC4134008 DOI: 10.3389/fmicb.2014.00403] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/17/2014] [Indexed: 11/30/2022] Open
Abstract
Replication slippage or slipped-strand mispairing involves the misalignment of DNA strands during the replication of repeated DNA sequences, and can lead to genetic rearrangements such as microsatellite instability. Here, we show that PolB and PolD replicative DNA polymerases from the archaeal model Pyrococcus abyssi (Pab) slip in vitro during replication of a single-stranded DNA template carrying a hairpin structure and short direct repeats. We find that this occurs in both their wild-type (exo+) and exonuclease deficient (exo-) forms. The slippage behavior of PabPolB and PabPolD, probably due to limited strand displacement activity, resembles that observed for the high fidelity P. furiosus (Pfu) DNA polymerase. The presence of PabPCNA inhibited PabPolB and PabPolD slippage. We propose a model whereby PabPCNA stimulates strand displacement activity and polymerase progression through the hairpin, thus permitting the error-free replication of repetitive sequences.
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Affiliation(s)
- Melissa Castillo-Lizardo
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Universidad de Malaga Málaga, Spain
| | - Ghislaine Henneke
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Institut Français de Recherche pour l'Exploitation de la Mer, Université de Bretagne Occidentale Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Enrique Viguera
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Universidad de Malaga Málaga, Spain
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10
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Vidaurre S, Fitzpatrick C, Burzio VA, Briones M, Villota C, Villegas J, Echenique J, Oliveira-Cruz L, Araya M, Borgna V, Socías T, Lopez C, Avila R, Burzio LO. Down-regulation of the antisense mitochondrial non-coding RNAs (ncRNAs) is a unique vulnerability of cancer cells and a potential target for cancer therapy. J Biol Chem 2014; 289:27182-27198. [PMID: 25100722 PMCID: PMC4175353 DOI: 10.1074/jbc.m114.558841] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hallmarks of cancer are fundamental principles involved in cancer progression. We propose an additional generalized hallmark of malignant transformation corresponding to the differential expression of a family of mitochondrial ncRNAs (ncmtRNAs) that comprises sense and antisense members, all of which contain stem-loop structures. Normal proliferating cells express sense (SncmtRNA) and antisense (ASncmtRNA) transcripts. In contrast, the ASncmtRNAs are down-regulated in tumor cells regardless of tissue of origin. Here we show that knockdown of the low copy number of the ASncmtRNAs in several tumor cell lines induces cell death by apoptosis without affecting the viability of normal cells. In addition, knockdown of ASncmtRNAs potentiates apoptotic cell death by inhibiting survivin expression, a member of the inhibitor of apoptosis (IAP) family. Down-regulation of survivin is at the translational level and is probably mediated by microRNAs generated by dicing of the double-stranded stem of the ASncmtRNAs, as suggested by evidence presented here, in which the ASncmtRNAs are bound to Dicer and knockdown of the ASncmtRNAs reduces reporter luciferase activity in a vector carrying the 3′-UTR of survivin mRNA. Taken together, down-regulation of the ASncmtRNAs constitutes a vulnerability or Achilles' heel of cancer cells, suggesting that the ASncmtRNAs are promising targets for cancer therapy.
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Affiliation(s)
- Soledad Vidaurre
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo ÓHiggins, General Gana 1702, Santiago, Chile
| | - Christopher Fitzpatrick
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Fundación Ciencia para la Vida, Zañartu 1482, Ñuñoa, Santiago 7780272, Chile,; Facultad de Ciencias Biológicas and Universidad Andrés Bello, República 252, Santiago 8370134, Chile
| | - Verónica A Burzio
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Fundación Ciencia para la Vida, Zañartu 1482, Ñuñoa, Santiago 7780272, Chile,; Facultad de Ciencias Biológicas and Universidad Andrés Bello, República 252, Santiago 8370134, Chile.
| | - Macarena Briones
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Facultad de Ciencias Biológicas and Universidad Andrés Bello, República 252, Santiago 8370134, Chile
| | - Claudio Villota
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Fundación Ciencia para la Vida, Zañartu 1482, Ñuñoa, Santiago 7780272, Chile,; Facultad de Ciencias Biológicas and Universidad Andrés Bello, República 252, Santiago 8370134, Chile
| | - Jaime Villegas
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Fundación Ciencia para la Vida, Zañartu 1482, Ñuñoa, Santiago 7780272, Chile,; Facultad de Ciencias Biológicas and Universidad Andrés Bello, República 252, Santiago 8370134, Chile
| | - Javiera Echenique
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Luciana Oliveira-Cruz
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Fundación Ciencia para la Vida, Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Mariela Araya
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Vincenzo Borgna
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Facultad de Medicina, Universidad Andrés Bello, República 252, Santiago 8370134, Chile, and
| | - Teresa Socías
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Constanza Lopez
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Rodolfo Avila
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Luis O Burzio
- Andes Biotechnologies SA and Zañartu 1482, Ñuñoa, Santiago 7780272, Chile; Fundación Ciencia para la Vida, Zañartu 1482, Ñuñoa, Santiago 7780272, Chile,; Facultad de Ciencias Biológicas and Universidad Andrés Bello, República 252, Santiago 8370134, Chile.
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11
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Mukudai Y, Kubota S, Eguchi T, Sumiyoshi K, Janune D, Kondo S, Shintani S, Takigawa M. A coding RNA segment that enhances the ribosomal recruitment of chicken ccn1 mRNA. J Cell Biochem 2011; 111:1607-18. [PMID: 21053272 DOI: 10.1002/jcb.22894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CCN1, a member of the CCN family of proteins, plays important physiological or pathological roles in a variety of tissues. In the present study, we initially found a highly guanine-cytosine (GC)-rich region of approximately 200 bp near the 5'-end of the open reading frame, which was always truncated by amplification of the corresponding cDNA region through the conventional polymerase chain reaction. An RNA in vitro folding assay and selective ribonuclease digestion of the corresponding segment of the ccn1 mRNA confirmed the involvement of a stable secondary structure. Subsequent RNA electromobility-shift assays demonstrated the specific binding of some cytoplasmic factor(s) in chicken embryo fibroblasts to the RNA segment. Moreover, the corresponding cDNA fragment strongly enhanced the expression of the reporter gene in cis at the 5'-end, but did not do so at the 3'-end. According to the results of a ribosomal assembly test, the effect of the mRNA segment can predominantly be ascribed to the enhancement of transport and/or entry of the mRNA into the ribosome. Finally, the minimal GC-rich mRNA segment that was predicted and demonstrated to form a secondary structure was confirmed to be a functional regulatory element. Thus, we here uncover a novel dual-functionality of the mRNA segment in the ccn1 open reading frame, which segment acts as a cis-element that mediates posttranscriptional gene regulation, while retaining the information for the amino acid sequence of the resultant protein.
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Affiliation(s)
- Yoshiki Mukudai
- Biodental Research Center, Okayama University Dental School, Okayama, Japan
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12
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Bryan A, Swanson MS. Oligonucleotides stimulate genomic alterations of Legionella pneumophila. Mol Microbiol 2011; 80:231-47. [PMID: 21306445 DOI: 10.1111/j.1365-2958.2011.07573.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Genetic variation generates diversity in all kingdoms of life. The corresponding mechanisms can also be harnessed for laboratory studies of fundamental cellular processes. Here we report that oligonucleotides (oligos) generate mutations on the Legionella pneumophila chromosome by a mechanism that requires homologous DNA, but not RecA, RadA or any known phage recombinase. Instead we propose that DNA replication contributes, as oligo-induced mutagenesis required ≥ 21 nucleotides of homology, was strand-dependent, and was most efficient in exponential phase. Mutagenesis did not require canonical 5' phosphate or 3' hydroxyl groups, but the primosomal protein PriA and DNA Pol I contributed. After electroporation, oligos stimulated excision of 2.1 kb of chromosomal DNA or insertion of 18 bp, and non-homologous flanking sequences were also processed. We exploited this endogenous activity to generate chromosomal deletions and to insert an epitope into a chromosomal coding sequence. Compared with Escherichia coli, L. pneumophila encodes fewer canonical single-stranded exonucleases, and the frequency of mutagenesis increased substantially when either its RecJ and ExoVII nucleases were inactivated or the oligos modified by nuclease-resistant bases. In addition to genetic engineering, oligo-induced mutagenesis may have evolutionary implications as a mechanism to incorporate divergent DNA sequences with only short regions of homology.
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Affiliation(s)
- Andrew Bryan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109-5620, USA
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13
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Touzain F, Denamur E, Médigue C, Barbe V, El Karoui M, Petit MA. Small variable segments constitute a major type of diversity of bacterial genomes at the species level. Genome Biol 2010; 11:R45. [PMID: 20433696 PMCID: PMC2884548 DOI: 10.1186/gb-2010-11-4-r45] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 03/15/2010] [Accepted: 04/30/2010] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. RESULTS We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed. CONCLUSIONS This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes.
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Affiliation(s)
- Fabrice Touzain
- INRA, UMR1319, Micalis, Bat 222, Jouy en Josas, 78350, France
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14
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Zepeda MYB, Alessandri K, Murat D, El Amri C, Dassa E. C-terminal domain of the Uup ATP-binding cassette ATPase is an essential folding domain that binds to DNA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:755-61. [DOI: 10.1016/j.bbapap.2009.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/12/2009] [Accepted: 11/19/2009] [Indexed: 10/20/2022]
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15
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Yuan Q, McHenry CS. Strand displacement by DNA polymerase III occurs through a tau-psi-chi link to single-stranded DNA-binding protein coating the lagging strand template. J Biol Chem 2009; 284:31672-9. [PMID: 19749191 DOI: 10.1074/jbc.m109.050740] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of gamma-complex to support the reaction in the absence of tau. However, if gamma-complex is present to load beta(2), a truncated tau protein containing only domains III-V will suffice. This truncated protein is sufficient to bind both the alpha subunit of DNA polymerase (Pol) III and chipsi. This is reminiscent of the minimal requirements for Pol III to replicate short single-stranded DNA-binding protein (SSB)-coated templates where tau is only required to serve as a scaffold to hold Pol III and chi in the same complex (Glover, B., and McHenry, C. (1998) J. Biol. Chem. 273, 23476-23484). We propose a model in which strand displacement by DNA polymerase III holoenzyme depends upon a Pol III-tau-psi-chi-SSB binding network, where SSB is bound to the displaced strand, stabilizing the Pol III-template interaction. The same interaction network is probably important for stabilizing the leading strand polymerase interactions with authentic replication forks. The specificity constant (k(cat)/K(m)) for the strand displacement reaction is approximately 300-fold less favorable than reactions on single-stranded templates and proceeds with a slower rate (150 nucleotides/s) and only moderate processivity (approximately 300 nucleotides). PriA, the initiator of replication restart on collapsed or misassembled replication forks, blocks the strand displacement reaction, even if added to an ongoing reaction.
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Affiliation(s)
- Quan Yuan
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
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16
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Krishnan NM, Rao BJ. A comparative approach to elucidate chloroplast genome replication. BMC Genomics 2009; 10:237. [PMID: 19457260 PMCID: PMC2695485 DOI: 10.1186/1471-2164-10-237] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 05/20/2009] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Electron microscopy analyses of replicating chloroplast molecules earlier predicted bidirectional Cairns replication as the prevalent mechanism, perhaps followed by rounds of a rolling circle mechanism. This standard model is being challenged by the recent proposition of homologous recombination-mediated replication in chloroplasts. RESULTS We address this issue in our current study by analyzing nucleotide composition in genome regions between known replication origins, with an aim to reveal any adenine to guanine deamination gradients. These gradual linear gradients typically result from the accumulation of deaminations over the time spent single-stranded by one of the strands of the circular molecule during replication and can, therefore, be used to model the course of replication. Our linear regression analyses on the nucleotide compositions of the non-coding regions and the synonymous third codon position of coding regions, between pairs of replication origins, reveal the existence of significant adenine to guanine deamination gradients in portions overlapping the Small Single Copy (SSC) and the Large Single Copy (LSC) regions between inverted repeats. These gradients increase bi-directionally from the center of each region towards the respective ends, suggesting that both the strands were left single-stranded during replication. CONCLUSION Single-stranded regions of the genome and gradients in time that these regions are left single-stranded, as revealed by our nucleotide composition analyses, appear to converge with the original bi-directional dual displacement loop model and restore evidence for its existence as the primary mechanism. Other proposed faster modes such as homologous recombination and rolling circle initiation could exist in addition to this primary mechanism to facilitate homoplasmy among the intra-cellular chloroplast population.
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Affiliation(s)
- Neeraja M Krishnan
- B-202, Department of Biological Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha road, Colaba, Mumbai 400 005, India
- Current address: Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
| | - Basuthkar J Rao
- B-202, Department of Biological Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha road, Colaba, Mumbai 400 005, India
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17
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Villegas J, Burzio V, Villota C, Landerer E, Martinez R, Santander M, Martinez R, Pinto R, Vera MI, Boccardo E, Villa LL, Burzio LO. Expression of a novel non-coding mitochondrial RNA in human proliferating cells. Nucleic Acids Res 2007; 35:7336-47. [PMID: 17962305 PMCID: PMC2175360 DOI: 10.1093/nar/gkm863] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Previously, we reported the presence in mouse cells of a mitochondrial RNA which contains an inverted repeat (IR) of 121 nucleotides (nt) covalently linked to the 5′ end of the mitochondrial 16S RNA (16S mtrRNA). Here, we report the structure of an equivalent transcript of 2374 nt which is over-expressed in human proliferating cells but not in resting cells. The transcript contains a hairpin structure comprising an IR of 815 nt linked to the 5′ end of the 16S mtrRNA and forming a long double-stranded structure or stem and a loop of 40 nt. The stem is resistant to RNase A and can be detected and isolated after digestion with the enzyme. This novel transcript is a non-coding RNA (ncRNA) and several evidences suggest that the transcript is synthesized in mitochondria. The expression of this transcript can be induced in resting lymphocytes stimulated with phytohaemagglutinin (PHA). Moreover, aphidicolin treatment of DU145 cells reversibly blocks proliferation and expression of the transcript. If the drug is removed, the cells re-assume proliferation and over-express the ncmtRNA. These results suggest that the expression of the ncmtRNA correlates with the replicative state of the cell and it may play a role in cell proliferation.
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18
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Litman GW, Dishaw LJ, Cannon JP, Haire RN, Rast JP. Alternative mechanisms of immune receptor diversity. Curr Opin Immunol 2007; 19:526-34. [PMID: 17703932 PMCID: PMC2065753 DOI: 10.1016/j.coi.2007.07.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 07/02/2007] [Accepted: 07/02/2007] [Indexed: 01/30/2023]
Abstract
Our views of both innate and adaptive immunity have been significantly modified by recent studies of immune receptors and immunity in protostomes, invertebrate deuterostomes, and jawless vertebrates. Extraordinary variation in the means whereby organisms recognize pathogens has been revealed by a series of recent findings, including: novel forms of familiar immune receptors, high genetic polymorphism for new receptor types, germline rearrangement for non-Ig domain receptors, somatic variation of germline-encoded receptors, and unusually complex alternative splicing of genes with both immune and non-immune roles. Collectively, these observations underscore heretofore unrecognized pathways in the evolution of immune recognition and suggest universal processes by which immune systems co-opt and integrate existing cellular mechanisms to effect diverse recognition functions.
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Affiliation(s)
- Gary W Litman
- Department of Molecular Genetics, All Children's Hospital, 801 Sixth Street South, St. Petersburg, FL 33701, United States.
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19
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Brenet F, Dussault N, Delfino C, Boudouresque F, Chinot O, Martin PM, Ouafik LH. Identification of secondary structure in the 5′-untranslated region of the human adrenomedullin mRNA with implications for the regulation of mRNA translation. Oncogene 2006; 25:6510-9. [PMID: 16715138 DOI: 10.1038/sj.onc.1209672] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adrenomedullin (AM) is a multifunctional regulatory peptide with important angiogenic and mitogenic properties. Here we identify a region of stable secondary structure in the 5'-untranslated region (5' UTR) of human AM mRNA. Reverse transcriptase-polymerase chain reaction of the 5' UTR consistently resulted, in addition to the product with the expected size of 155 base pair (bp), in a second product with an approximately 65-bp deletion from the central region of the 5' UTR, suggesting the presence of a secondary structure. The presence of a stem-loop structure was confirmed by probing the 5' UTR with RNases with selectivity for single- or double-stranded RNA. We investigated the role of this stem-loop structure in expression of luciferase reporter gene in cultured cell lines. Reporter assays using a chimeric mRNA that combined luciferase and the 5' UTR of AM mRNA demonstrated a dramatic decrease of the reporter activity owing to a decreased translation, whereas the deletion of the stem-loop structure localized between nt +31 and +95 from the cap site led to the recovery of activity. Gel migration shift assays using cytosolic extracts from mammalian cell lines demonstrate a specific binding of a cytosolic protein to riboprobes containing the 5' UTR of AM but not to riboprobes either corresponding to other areas of the message or containing the 5' UTR but lacking the region of secondary structure. Although we conclude that the 5' UTR of the human AM mRNA can modulate the translation of AM mRNA in vivo, and that the predicted stem-loop structure is necessary for this inhibition, the functional consequences of the cis element-binding activity remain to be determined.
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Affiliation(s)
- F Brenet
- Laboratoire de Cancérologie Expérimentale, Inserm EMI 0359, Université de la Méditerranée, Aix-Marseille II, Marseille Cedex 20, France
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20
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Abstract
Repetitive DNA sequences are abundant in eukaryotic genomes, and many of these sequences have the potential to adopt non-B DNA conformations. Genes harboring non-B DNA structure-forming sequences increase the risk of genetic instability and thus are associated with human diseases. In this review, we discuss putative mechanisms responsible for genetic instability events occurring at these non-B DNA structures, with a focus on hairpins, left-handed Z-DNA, and intramolecular triplexes or H-DNA. Slippage and misalignment are the most common events leading to DNA structure-induced mutagenesis. However, a number of other mechanisms of genetic instability have been proposed based on the finding that these structures not only induce expansions and deletions, but can also induce DNA strand breaks and rearrangements. The available data implicate a variety of proteins, such as mismatch repair proteins, nucleotide excision repair proteins, topoisomerases, and structure specific-nucleases in the processing of these mutagenic DNA structures. The potential mechanisms of genetic instability induced by these structures and their contribution to human diseases are discussed.
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Affiliation(s)
- Guliang Wang
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, 1808 Park Road 1-C, P.O. Box 389, Smithville, 78957, USA
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21
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Nagata Y, Kawaguchi G, Tago YI, Imai M, Watanabe T, Sakurai S, Ihara M, Kawata M, Yamamoto K. Absence of strand bias for deletion mutagenesis during chromosomal leading and lagging strand replication in Escherichia coli. Genes Genet Syst 2005; 80:1-8. [PMID: 15824450 DOI: 10.1266/ggs.80.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Investigations were carried out to determine whether both DNA strands involved in Escherichia coli chromosomal DNA replication are replicated with similar accuracy. Experiments consisted of measuring the forward mutation rate from tonB(+) to tonB(-) in pairs of polA deficient strains in which the chromosomal target gene tonB was oriented in the two possible directions relative to the origin of replication, oriC. Within these pairs, the tonB sequence would be subjected to leading strand replication in one orientation and to lagging strand replication in the other. The most common tonB mutations in the polA1 strain were deletions followed by frameshifts. Among the deletions, a strong hotspot site with a 13-base deletion in the polA1 strains accounted for 18 of the 33 deletions in the one orientation, and 31 of the 58 deletions in the other. The results suggested that the two strands were replicated with equal or similar accuracy for deletion formation.
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Affiliation(s)
- Yuki Nagata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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22
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Abstract
A novel method, based upon primer extension, has been developed for measuring the reopening temperature of a single type of DNA hairpin structure. Two DNA oligonucleotides have been utilized and designated as primers 1 and 2. Primer 1, with its 5- and 3'-termini fully complementary to the hairpin flanking sequences, was used to evaluate primer extension conditions, and primer 2, with its 3'-end competing with the DNA hairpin stem, was used to detect the DNA hairpin reopening temperature. A single DNA hairpin structure was formed on the DNA template by thermal denaturation and renaturation, and this hairpin structure was predicted to prevent the annealing of the 3'-end of primer 2 with the template DNA, which leads to no primer extension. By incubating at different temperatures, the DNA hairpin structure can be reopened at a particular temperature where the primer extension can be carried out. This resulted in the appearance of double-stranded DNA that was detected on an agarose gel. This temperature is defined here as the hairpin reopening temperature.
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Affiliation(s)
- Xuefeng Pan
- Institute of Microbiology, The Chinese Academy of Sciences, Beijing, China. ,
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23
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Barry AE, Leliwa A, Choi M, Nielsen KM, Hartl DL, Day KP. DNA sequence artifacts and the estimation of time to the most recent common ancestor (TMRCA) of Plasmodium falciparum. Mol Biochem Parasitol 2003; 130:143-7. [PMID: 12946852 DOI: 10.1016/s0166-6851(03)00164-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Alyssa E Barry
- The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
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24
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Wagle MD, Sen S, Rao BJ. Local repeat sequence organization of an intergenic spacer in the chloroplast genome of Chlamydomonas reinhardtii leads to DNA expansion and sequence scrambling: a complex mode of "copy-choice replication"? J Biosci 2001; 26:583-94. [PMID: 11807289 DOI: 10.1007/bf02704757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Parent-specific, randomly amplified polymorphic DNA (RAPD) markers were obtained from total genomic DNA of Chlamydomonas reinhardtii. Such parent-specific RAPD bands (genomic fingerprints) segregated uniparentally (through mt+) in a cross between a pair of polymorphic interfertile strains of Chlamydomonas (C. reinhardtii and C. minnesotti), suggesting that they originated from the chloroplast genome. Southern analysis mapped the RAPD-markers to the chloroplast genome. One of the RAPD-markers, "P2" (1.6 kb) was cloned, sequenced and was fine mapped to the 3 kb region encompassing 3' end of 23S, full 5S and intergenic region between 5S and psbA. This region seems divergent enough between the two parents, such that a specific PCR designed for a parental specific chloroplast sequence within this region, amplified a marker in that parent only and not in the other, indicating the utility of RAPD-scan for locating the genomic regions of sequence divergence. Remarkably, the RAPD-product, "P2" seems to have originated from a PCR-amplification of a much smaller (about 600 bp), but highly repeat-rich (direct and inverted) domain of the 3 kb region in a manner that yielded no linear sequence alignment with its own template sequence. The amplification yielded the same uniquely "sequence-scrambled" product, whether the template used for PCR was total cellular DNA, chloroplast DNA or a plasmid clone DNA corresponding to that region. The PCR product, a "unique" new sequence, had lost the repetitive organization of the template genome where it had originated from and perhaps represented a "complex path" of copy-choice replication.
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Affiliation(s)
- M D Wagle
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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25
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Viguera E, Canceill D, Ehrlich SD. In vitro replication slippage by DNA polymerases from thermophilic organisms. J Mol Biol 2001; 312:323-33. [PMID: 11554789 DOI: 10.1006/jmbi.2001.4943] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Replication slippage of DNA polymerases is a potential source of spontaneous genetic rearrangements in prokaryotic and eukaryotic cells. Here we show that different thermostable DNA polymerases undergo replication slippage in vitro, during single-round replication of a single-stranded DNA template carrying a hairpin structure. Low-fidelity polymerases, such as Thermus aquaticus (Taq), high-fidelity polymerases, such as Pyrococcus furiosus (Pfu) and a highly thermostable polymerase from Pyrococcus abyssi (Pyra exo(-)) undergo slippage. Thermococcus litoralis DNA polymerase (Vent) is also able to slip; however, slippage can be inhibited when its strand-displacement activity is induced. Moreover, DNA polymerases that have a constitutive strand-displacement activity, such as Bacillus stearothermophilus DNA polymerase (Bst), do not slip. Polymerases that slip during single-round replication generate hairpin deletions during PCR amplification, with the exception of Vent polymerase because its strand-displacement activity is induced under these conditions. We show that these hairpin deletions occurring during PCR are due to replication slippage, and not to a previously proposed process involving polymerization across the hairpin base.
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Affiliation(s)
- E Viguera
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert 78350 Jouy-en-Josas, France.
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26
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Viguera E, Canceill D, Ehrlich SD. Replication slippage involves DNA polymerase pausing and dissociation. EMBO J 2001; 20:2587-95. [PMID: 11350948 PMCID: PMC125466 DOI: 10.1093/emboj/20.10.2587] [Citation(s) in RCA: 206] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome rearrangements can take place by a process known as replication slippage or copy-choice recombination. The slippage occurs between repeated sequences in both prokaryotes and eukaryotes, and is invoked to explain microsatellite instability, which is related to several human diseases. We analysed the molecular mechanism of slippage between short direct repeats, using in vitro replication of a single-stranded DNA template that mimics the lagging strand synthesis. We show that slippage involves DNA polymerase pausing, which must take place within the direct repeat, and that the pausing polymerase dissociates from the DNA. We also present evidence that, upon polymerase dissociation, only the terminal portion of the newly synthesized strand separates from the template and anneals to another direct repeat. Resumption of DNA replication then completes the slippage process.
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Affiliation(s)
- E Viguera
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78350 Jouy en Josas, France.
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27
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Bzymek M, Lovett ST. Instability of repetitive DNA sequences: the role of replication in multiple mechanisms. Proc Natl Acad Sci U S A 2001; 98:8319-25. [PMID: 11459970 PMCID: PMC37438 DOI: 10.1073/pnas.111008398] [Citation(s) in RCA: 248] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rearrangements between tandem sequence homologies of various lengths are a major source of genomic change and can be deleterious to the organism. These rearrangements can result in either deletion or duplication of genetic material flanked by direct sequence repeats. Molecular genetic analysis of repetitive sequence instability in Escherichia coli has provided several clues to the underlying mechanisms of these rearrangements. We present evidence for three mechanisms of RecA-independent sequence rearrangements: simple replication slippage, sister-chromosome exchange-associated slippage, and single-strand annealing. We discuss the constraints of these mechanisms and contrast their properties with RecA-dependent homologous recombination. Replication plays a critical role in the two slipped misalignment mechanisms, and difficulties in replication appear to trigger rearrangements via all these mechanisms.
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Affiliation(s)
- M Bzymek
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
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28
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Bzymek M, Lovett ST. Evidence for two mechanisms of palindrome-stimulated deletion in Escherichia coli: single-strand annealing and replication slipped mispairing. Genetics 2001; 158:527-40. [PMID: 11404319 PMCID: PMC1461685 DOI: 10.1093/genetics/158.2.527] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spontaneous deletion mutations often occur at short direct repeats that flank inverted repeat sequences. Inverted repeats may initiate genetic rearrangements by formation of hairpin secondary structures that block DNA polymerases or are processed by structure-specific endonucleases. We have investigated the ability of inverted repeat sequences to stimulate deletion of flanking direct repeats in Escherichia coli. Propensity for cruciform extrusion in duplex DNA correlated with stimulation of flanking deletion, which was partially sbcD dependent. We propose two mechanisms for palindrome-stimulated deletion, SbcCD dependent and SbcCD independent. The SbcCD-dependent mechanism is initiated by SbcCD cleavage of cruciforms in duplex DNA followed by RecA-independent single-strand annealing at the flanking direct repeats, generating a deletion. Analysis of deletion endpoints is consistent with this model. We propose that the SbcCD-independent pathway involves replication slipped mispairing, evoked from stalling at hairpin structures formed on the single-stranded lagging-strand template. The skew of SbcCD-independent deletion endpoints with respect to the direction of replication supports this hypothesis. Surprisingly, even in the absence of palindromes, SbcD affected the location of deletion endpoints, suggesting that SbcCD-mediated strand processing may also accompany deletion unassociated with secondary structures.
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Affiliation(s)
- M Bzymek
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-0110, USA
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29
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Bruand C, Bidnenko V, Ehrlich SD. Replication mutations differentially enhance RecA-dependent and RecA-independent recombination between tandem repeats in Bacillus subtilis. Mol Microbiol 2001; 39:1248-58. [PMID: 11251841 DOI: 10.1111/j.1365-2958.2001.02312.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied DNA recombination between 513 bp tandem direct repeats present in a kanamycin resistance gene inserted in the Bacillus subtilis chromosome. Tandem repeat deletion was not significantly affected by a recA mutation. However, recombination was stimulated by mutations in genes encoding replication proteins, including the primosomal proteins DnaB, DnaD and the DnaG primase, the putative DNA polymerase III subunits PolC, DnaN and DnaX, as well as the DNA polymerase DnaE. Hyper-recombination was found to be dependent on RecA in the dnaE, dnaN and dnaX mutants, whereas the dnaG and dnaD mutants stimulated recombination independently of RecA. Altogether, these data show that both RecA-dependent and RecA-independent mechanisms contribute to recombination between tandem repeats in B. subtilis and that both types of recombination are stimulated by replication mutations.
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Affiliation(s)
- C Bruand
- Laboratoire de Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France.
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30
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Pluciennik A, Iyer RR, Parniewski P, Wells RD. Tandem duplication. A novel type of triplet repeat instability. J Biol Chem 2000; 275:28386-97. [PMID: 10877999 DOI: 10.1074/jbc.m000154200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Triplet repeat sequence (TRS) inserts containing (CTG.CAG)(n) (17-175 units in length) were tandemly duplicated when propagated in plasmids in Escherichia coli. The products of this novel type of TRS genetic instability are tracts of as many as 34 multiple units, which contain the entire TRS as well as 129 base pairs of nonrepetitive flanking sequence. The duplication process required the presence of two or more TRS-containing units. Close proximity (170 base pairs) of the TRS to the R6K gamma origin of replication of the pUTminiTn5Cm-derived constructs stimulated the tandem duplication process. These events are proposed to occur due to secondary structure formation, stalling of DNA synthesis, and slippage-mediated misalignment of the complementary strands relative to each other during DNA replication. This mechanism may account for the TRS-associated duplications in protein kinase and metalloprotease genes in neuroblastomas and melanomas, as well as the massive repeat expansions in type II triplet repeat neurological diseases.
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Affiliation(s)
- A Pluciennik
- Institute of Biosciences and Technology, Center for Genome Research, Texas A&M University, Texas Medical Center, Houston, Texas 77030, USA
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31
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Reddy M, Gowrishankar J. Characterization of the uup locus and its role in transposon excisions and tandem repeat deletions in Escherichia coli. J Bacteriol 2000; 182:1978-86. [PMID: 10715006 PMCID: PMC101901 DOI: 10.1128/jb.182.7.1978-1986.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Null mutations in the Escherichia coli uup locus (at 21.8 min) serve to increase the frequency of RecA-independent precise excision of transposable elements such as Tn10 and to reduce the plaque size of bacteriophage Mu (Uup(-) phenotype). By the combined approaches of physical mapping of the mutations, complementation analyses, and protein overexpression from cloned gene fragments, we have demonstrated in this study that the Uup(-) phenotype is the consequence of the absence of expression of the downstream gene (uup) of a two-gene operon, caused either directly by insertions in uup or indirectly by the polar effect of insertions in the upstream gene (ycbY). The promoter for uup was mapped upstream of ycbY by primer extension analysis on cellular RNA, and assays of reporter gene expression indicated that it is a moderately active, constitutive promoter. The uup mutations were also shown to increase, in a RecA-independent manner, the frequencies of nearly precise excision of Tn10 derivatives and of the deletion of one copy of a chromosomal tandem repeat, suggesting the existence of a shared step or intermediate in the pathways of these latter events and that of precise excision. Finally, we found that mutations that increase the frequency of precise excision of Tn10 are divisible into two categories, depending upon whether they did (uup, ssb, polA, and topA) or did not (mutHLS, dam, and uvrD) also increase precise excision frequency of the mini-Tn10 derivatives. It is suggested that the differential response of mini-Tn10 and Tn10 to the second category of mutations is related to the presence, respectively, of perfect and of imperfect terminal inverted repeats in them.
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Affiliation(s)
- M Reddy
- Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
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32
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Abstract
Replication arrests are associated with genome rearrangements, which result from either homologous or non-homologous recombination. Interestingly, proteins involved in homologous recombination are able to convert an arrested replication fork into a recombination intermediate, which promotes replication restart and thus presumably prevents genome rearrangements.
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Affiliation(s)
- B Michel
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, 78352 Jouy en Josas Cedex, France.
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33
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Backert S. Strand switching during rolling circle replication of plasmid-like DNA circles in the mitochondria of the higher plant Chenopodium album (L.). Plasmid 2000; 43:166-70. [PMID: 10686137 DOI: 10.1006/plas.1999.1437] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of sigma-like mitochondrial DNA molecules prepared from suspension cultured cells of Chenopodium album (L.) was studied by electron microscopy. These molecules were highly variable in size, ranging from about 1 to 104 kb, and had single- and double-stranded regions typical for rolling circle replicating intermediates. Partial denaturation studies confirmed that these structures constitute rolling circles. Close inspection of the circle-tail junctions of the replication fork at high magnification suggests that in circles with a double-stranded tail, both strands of the tail seem to be covalently attached to the circle in about 27% of the molecules. This observation can be explained by a phenomenon called strand switching or strand splippage during rolling circle replication, similar to a mechanism proposed for bacterial replicons or in vitro replicating constructs harboring bacteriophage T4 replication origins.
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MESH Headings
- Chenopodiaceae/genetics
- Chenopodiaceae/ultrastructure
- DNA Replication
- DNA, Circular/biosynthesis
- DNA, Circular/ultrastructure
- DNA, Mitochondrial/biosynthesis
- DNA, Mitochondrial/ultrastructure
- DNA, Plant/biosynthesis
- DNA, Plant/ultrastructure
- DNA, Single-Stranded/biosynthesis
- DNA, Single-Stranded/ultrastructure
- Electrophoresis, Gel, Pulsed-Field
- Microscopy, Electron
- Plasmids/metabolism
- Plasmids/ultrastructure
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Affiliation(s)
- S Backert
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, Berlin, D-10115, Germany.
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Yao N, Hurwitz J, O'Donnell M. Dynamics of beta and proliferating cell nuclear antigen sliding clamps in traversing DNA secondary structure. J Biol Chem 2000; 275:1421-32. [PMID: 10625694 DOI: 10.1074/jbc.275.2.1421] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromosomal replicases of cellular organisms utilize a ring shaped protein that encircles DNA as a mobile tether for high processivity in DNA synthesis. These "sliding clamps" have sufficiently large linear diameters to encircle duplex DNA and are perhaps even large enough to slide over certain DNA secondary structural elements. This report examines the Escherichia coli beta and human proliferating cell nuclear antigen clamps for their ability to slide over various DNA secondary structures. The results show that these clamps are capable of traversing a 13-nucleotide ssDNA loop, a 4-base pair stem-loop, a 4-nucleotide 5' tail, and a 15-mer bubble within the duplex. However, upon increasing the size of these structures (20-nucleotide loop, 12-base pair stem-loop, 28-nucleotide 5' tail, and 20-nucleotide bubble) the sliding motion of the beta and proliferating cell nuclear antigen over these elements is halted. Studies of the E. coli replicase, DNA polymerase III holoenzyme, in chain elongation with the beta clamp demonstrate that upon encounter with an oligonucleotide annealed in its path, it traverses the duplex and resumes synthesis on the 3' terminus of the oligonucleotide. This sliding and resumption of synthesis occurs even when the oligonucleotide contains a secondary structure element, provided the beta clamp can traverse the structure. However, upon encounter with a downstream oligonucleotide containing a large internal secondary structure, the holoenzyme clears the obstacle by strand displacing the oligonucleotide from the template. Implications of these protein dynamics to DNA transactions are discussed.
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Affiliation(s)
- N Yao
- Joan and Sanford I. Weill Graduate School of Medical Sciences of Cornell University, Microbiology Department, New York, New York 10021, USA
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35
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Waldman AS, Tran H, Goldsmith EC, Resnick MA. Long inverted repeats are an at-risk motif for recombination in mammalian cells. Genetics 1999; 153:1873-83. [PMID: 10581292 PMCID: PMC1460879 DOI: 10.1093/genetics/153.4.1873] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Certain DNA sequence motifs and structures can promote genomic instability. We have explored instability induced in mouse cells by long inverted repeats (LIRs). A cassette was constructed containing a herpes simplex virus thymidine kinase (tk) gene into which was inserted an LIR composed of two inverted copies of a 1.1-kb yeast URA3 gene sequence separated by a 200-bp spacer sequence. The tk gene was introduced into the genome of mouse Ltk(-) fibroblasts either by itself or in conjunction with a closely linked tk gene that was disrupted by an 8-bp XhoI linker insertion; rates of intrachromosomal homologous recombination between the markers were determined. Recombination between the two tk alleles was stimulated 5-fold by the LIR, as compared to a long direct repeat (LDR) insert, resulting in nearly 10(-5) events per cell per generation. Of the tk(+) segregants recovered from LIR-containing cell lines, 14% arose from gene conversions that eliminated the LIR, as compared to 3% of the tk(+) segregants from LDR cell lines, corresponding to a >20-fold increase in deletions at the LIR hotspot. Thus, an LIR, which is a common motif in mammalian genomes, is at risk for the stimulation of homologous recombination and possibly other genetic rearrangements.
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Affiliation(s)
- A S Waldman
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA.
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36
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Dyall J, Szabo P, Berns KI. Adeno-associated virus (AAV) site-specific integration: formation of AAV-AAVS1 junctions in an in vitro system. Proc Natl Acad Sci U S A 1999; 96:12849-54. [PMID: 10536011 PMCID: PMC23128 DOI: 10.1073/pnas.96.22.12849] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An in vitro system to study the mechanism of site-specific integration of adeno-associated virus (AAV) was developed. This system is based on two substrates, a linear or circular AAV donor and a circular acceptor containing the preintegration locus AAVS1. In the presence of HeLa extract and the His-Tag-purified Rep68 protein, specific covalent junctions between AAV and AAVS1 were formed and detected by PCR. The majority of the junctions were located within the Rep binding site of both the AAV and the AAVS1 substrates, underlining the involvement of the Rep protein. A limited amount of replication and the presence of nuclear factors promoted the efficiency of the reaction. The process was ATP-dependent, indicating that the helicase activity of Rep may be important in the formation of the junctions. According to current models of integration, the formation of the junctions would represent a first step in the process of AAV integration. This step could be crucial for the site specificity of the recombination event that leads to the integration of AAV into human chromosome 19 in vivo.
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Affiliation(s)
- J Dyall
- Department of Human Genetics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
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37
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Roth GE, Wattler S, Bornschein H, Lehmann M, Korge G. Structure and regulation of the salivary gland secretion protein gene Sgs-1 of Drosophila melanogaster. Genetics 1999; 153:753-62. [PMID: 10511555 PMCID: PMC1460785 DOI: 10.1093/genetics/153.2.753] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Drosophila melanogaster gene Sgs-1 belongs to the secretion protein genes, which are coordinately expressed in salivary glands of third instar larvae. Earlier analysis had implied that Sgs-1 is located at the 25B2-3 puff. We cloned Sgs-1 from a YAC covering 25B2-3. Despite using a variety of vectors and Escherichia coli strains, subcloning from the YAC led to deletions within the Sgs-1 coding region. Analysis of clonable and unclonable sequences revealed that Sgs-1 mainly consists of 48-bp tandem repeats encoding a threonine-rich protein. The Sgs-1 inserts from single lambda clones are heterogeneous in length, indicating that repeats are eliminated. By analyzing the expression of Sgs-1/lacZ fusions in transgenic flies, cis-regulatory elements of Sgs-1 were mapped to lie within 1 kb upstream of the transcriptional start site. Band shift assays revealed binding sites for the transcription factor fork head (FKH) and the factor secretion enhancer binding protein 3 (SEBP3) at positions that are functionally relevant. FKH and SEBP3 have been shown previously to be involved in the regulation of Sgs-3 and Sgs-4. Comparison of the levels of steady state RNA and of the transcription rates for Sgs-1 and Sgs-1/lacZ reporter genes indicates that Sgs-1 RNA is 100-fold more stable than Sgs-1/lacZ RNA. This has implications for the model of how Sgs transcripts accumulate in late third instar larvae.
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Affiliation(s)
- G E Roth
- Institut für Genetik, Freie Universität Berlin, 14195 Berlin, Germany.
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38
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Canceill D, Viguera E, Ehrlich SD. Replication slippage of different DNA polymerases is inversely related to their strand displacement efficiency. J Biol Chem 1999; 274:27481-90. [PMID: 10488082 DOI: 10.1074/jbc.274.39.27481] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication slippage is a particular type of error caused by DNA polymerases believed to occur both in bacterial and eukaryotic cells. Previous studies have shown that deletion events can occur in Escherichia coli by replication slippage between short duplications and that the main E. coli polymerase, DNA polymerase III holoenzyme is prone to such slippage. In this work, we present evidence that the two other DNA polymerases of E. coli, DNA polymerase I and DNA polymerase II, as well as polymerases of two phages, T4 (T4 pol) and T7 (T7 pol), undergo slippage in vitro, whereas DNA polymerase from another phage, Phi29, does not. Furthermore, we have measured the strand displacement activity of the different polymerases tested for slippage in the absence and in the presence of the E. coli single-stranded DNA-binding protein (SSB), and we show that: (i) polymerases having a strong strand displacement activity cannot slip (DNA polymerase from Phi29); (ii) polymerases devoid of any strand displacement activity slip very efficiently (DNA polymerase II and T4 pol); and (iii) stimulation of the strand displacement activity by E. coli SSB (DNA polymerase I and T7 pol), by phagic SSB (T4 pol), or by a mutation that affects the 3' --> 5' exonuclease domain (DNA polymerase II exo(-) and T7 pol exo(-)) is correlated with the inhibition of slippage. We propose that these observations can be interpreted in terms of a model, for which we have shown that high strand displacement activity of a polymerase diminishes its propensity to slip.
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Affiliation(s)
- D Canceill
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France.
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39
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Müller AE, Kamisugi Y, Grüneberg R, Niedenhof I, Hörold RJ, Meyer P. Palindromic sequences and A+T-rich DNA elements promote illegitimate recombination in Nicotiana tabacum. J Mol Biol 1999; 291:29-46. [PMID: 10438604 DOI: 10.1006/jmbi.1999.2957] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Illegitimate recombination is the prevailing molecular mechanism for the integration of recombinant DNA into the genome of most eukaryotic systems and the generation of deletions by intrachromosomal recombination. We developed a ?selectable marker system to screen for intrachromosomal illegitimate recombination events in order to assess the sequence and structure-specific requirements for illegitimate recombination in tobacco. In 12 illegitimate recombination products analysed, we found that all deletion termini localise to sites of palindromic structures or to A+T-rich DNA elements. All deletion termini showed microhomologies of two to six nucleotides. In three plants, the recombination products contained filler-DNA or an inversion of an endogenous segment. Our data strongly suggest that illegitimate recombination in plants is mediated by a DNA synthesis-dependent process, and that this mechanism is promoted by DNA regions that can form palindromic structures or facilitate DNA unwinding.
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40
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Hew Y, Grzelczak Z, Lau C, Keeley FW. Identification of a large region of secondary structure in the 3'-untranslated region of chicken elastin mRNA with implications for the regulation of mRNA stability. J Biol Chem 1999; 274:14415-21. [PMID: 10318866 DOI: 10.1074/jbc.274.20.14415] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synthesis of aortic elastin peaks in the perinatal period and then is strongly down-regulated with postnatal vascular development. Our laboratory has previously shown that changes in elastin mRNA stability contribute to this developmental decrease in elastin production. Here we identify a large region of stable secondary structure in the 3'-untranslated region (3'-UTR) of chicken elastin mRNA. Reverse transcriptase polymerase chain reaction or polymerase chain reaction amplification of the 3'-UTR consistently resulted in products with an approximately 328-bp deletion from the central region of the 3'-UTR, suggesting the presence of secondary structure. The presence of this structure was confirmed by probing the 3'-UTR with RNases with selectivity for single- or double-stranded RNA. Gel migration shift assays using cytosolic extracts from 2-day old chicken aorta demonstrate specific binding of a cytosolic protein to riboprobes containing the 3'-UTR of elastin but not to riboprobes either corresponding to other areas of the message or containing the 3'-UTR but lacking the region of secondary structure. Binding of cytosolic protein was particularly prominent in aortic extracts from 2-day old chickens, a time when elastin message is stable, as compared with 8- and 15-week old chickens, when the elastin message is relatively unstable, suggesting that this region of secondary structure may play a role in developmental regulation of stability of elastin mRNA.
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Affiliation(s)
- Y Hew
- Division of Cardiovascular Research, Research Institute, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1X8, Canada
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41
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Zaphiropoulos PG. Non-homologous recombination mediated by Thermus aquaticus DNA polymerase I. Evidence supporting a copy choice mechanism. Nucleic Acids Res 1998; 26:2843-8. [PMID: 9611226 PMCID: PMC147658 DOI: 10.1093/nar/26.12.2843] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RT-PCR amplification of P450 2C6 from rat liver, using primers in opposite orientations of exon 6, resulted in PCR products containing segments of exons joined at non-consensus splice sites. Moreover, many of the PCR products identified were composed of not only a single region containing exonic segments joined at non-consensus splice sites but, instead, of several repeats of the non-canonically joined region. To investigate whether these PCR products represent pre-existing molecules or are generated during the amplification process, the liver cDNA template was replaced by a plasmid containing the P450 2C6 cDNA. Surprisingly, PCR products containing repeats of non-canonically joined exonic segments were again revealed. In some cases the position of this non-canonical joining was a sequence of one or two identical nucleotides; however, there were also a number of products lacking any nucleotide identity at the position of joining. DNA nicking and/or DNA damage is thought to favour recombination during PCR, probably by misalignment of incomplete DNA strands; however, the presence of multiple repeats of the recombined region in the PCR products identified suggests a certain repetitiveness of the underlying mechanism. It is therefore proposed that these products result from a template switching event that occurs several times during a single polymerization step, following a rolling circle model of DNA synthesis.
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Affiliation(s)
- P G Zaphiropoulos
- Department of Bioscience, Center for Nutrition and Toxicology, Karolinska Institute, Novum, 141 57 Huddinge, Sweden.
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42
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Pâques F, Leung WY, Haber JE. Expansions and contractions in a tandem repeat induced by double-strand break repair. Mol Cell Biol 1998; 18:2045-54. [PMID: 9528777 PMCID: PMC121435 DOI: 10.1128/mcb.18.4.2045] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/1997] [Accepted: 01/16/1998] [Indexed: 02/07/2023] Open
Abstract
Repair of a double-strand break (DSB) in yeast can induce very frequent expansions and contractions in a tandem array of 375-bp repeats. These results strongly suggest that DSB repair can be a major source of amplification of tandemly repeated sequences. Most of the DSB repair events are not associated with crossover. Rearrangements appear in 50% of these repaired recipient molecules. In contrast, the donor template nearly always remains unchanged. Among the rare crossover events, similar rearrangements are found. These results cannot readily be explained by the gap repair model of Szostak et al. (J. W. Szostak, T. L. Orr-Weaver, R. J. Rothstein, and F. W. Stahl, Cell 33:25-35, 1983) but can be explained by synthesis-dependent strand annealing (SDSA) models that allow for crossover. Support for SDSA models is provided by a demonstration that a single DSB repair event can use two donor templates located on two different chromosomes.
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Affiliation(s)
- F Pâques
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110, USA
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43
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Lobachev KS, Shor BM, Tran HT, Taylor W, Keen JD, Resnick MA, Gordenin DA. Factors affecting inverted repeat stimulation of recombination and deletion in Saccharomyces cerevisiae. Genetics 1998; 148:1507-24. [PMID: 9560370 PMCID: PMC1460095 DOI: 10.1093/genetics/148.4.1507] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inverted DNA repeats are an at-risk motif for genetic instability that can induce both deletions and recombination in yeast. We investigated the role of the length of inverted repeats and size of the DNA separating the repeats for deletion and recombination. Stimulation of both deletion and recombination was directly related to the size of inverted repeats and inversely related to the size of intervening spacers. A perfect palindrome, formed by two 1.0-kb URA3-inverted repeats, increased intra- and interchromosomal recombination in the adjacent region 2,400-fold and 17,000-fold, respectively. The presence of a strong origin of replication in the spacer reduced both rates of deletion and recombination. These results support a model in which the stimulation of deletion and recombination by inverted repeats is initiated by a secondary structure formed between single-stranded DNA of inverted repeats during replication.
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Affiliation(s)
- K S Lobachev
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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44
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Villarroya M, Pérez-Roger I, Macián F, Armengod ME. Stationary phase induction of dnaN and recF, two genes of Escherichia coli involved in DNA replication and repair. EMBO J 1998; 17:1829-37. [PMID: 9501104 PMCID: PMC1170530 DOI: 10.1093/emboj/17.6.1829] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The beta subunit of DNA polymerase III holoenzyme, the Escherichia coli chromosomal replicase, is a sliding DNA clamp responsible for tethering the polymerase to DNA and endowing it with high processivity. The gene encoding beta, dnaN, maps between dnaA and recF, which are involved in initiation of DNA replication at oriC and resumption of DNA replication at disrupted replication forks, respectively. In exponentially growing cells, dnaN and recF are expressed predominantly from the dnaA promoters. However, we have found that stationary phase induction of the dnaN promoters drastically changes the expression pattern of the dnaA operon genes. As a striking consequence, synthesis of the beta subunit and RecF protein increases when cell metabolism is slowing down. Such an induction is dependent on the stationary phase sigma factor, RpoS, although the accumulation of this factor alone is not sufficient to activate the dnaN promoters. These promoters are located in DNA regions without static bending, and the -35 hexamer element is essential for their RpoS-dependent induction. Our results suggest that stationary phase-dependent mechanisms have evolved in order to coordinate expression of dnaN and recF independently of the dnaA regulatory region. These mechanisms might be part of a developmental programme aimed at maintaining DNA integrity under stress conditions.
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Affiliation(s)
- M Villarroya
- Instituto de Investigaciones Citológicas, Fundación Valenciana de Investigaciones Biomedicas, Valencia 46010, Spain
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45
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Slezarikova V, Masek F, Pirsel M, Sedliakova M. The pre-UV nutritional stresses increase UV resistance, decrease UV mutagenesis and inhibit excision repair. Mutat Res 1997; 385:213-22. [PMID: 9506890 DOI: 10.1016/s0921-8777(97)00044-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nutritional stresses applied to E. coli prior to UV irradiation increase UV resistance and decrease UV mutagenesis. This effect is uvrA-dependent and might reflect a more efficient excision of pyrimidine dimers [1]. The data presented here, however, indicate that after prestarvation for glucose or amino acids pyrimidine dimer excision (PDE) was partly inhibited. It appears that the stress conditions stimulate a mode of uvr-dependent tolerance of lesions, efficient and precise. Possible modes of PDE inhibition and lesion tolerance are discussed.
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Affiliation(s)
- V Slezarikova
- Department of Molecular Genetics, Cancer Research Institute, Slovak Academy of Sciences, Bratislava, Slovak Republic
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46
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Reddy M, Gowrishankar J. A genetic strategy to demonstrate the occurrence of spontaneous mutations in nondividing cells within colonies of Escherichia coli. Genetics 1997; 147:991-1001. [PMID: 9383047 PMCID: PMC1208273 DOI: 10.1093/genetics/147.3.991] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A genetic strategy was designed to examine the occurrence of mutations in stationary-phase populations. In this strategy, a parental population of cells is able to survive under both permissive and restrictive conditions whereas mutants at a particular target locus exhibit a conditional-lethal phenotype. Thus, by growing the population to stationary phase under restrictive conditions and then shifting it to permissive conditions, mutations that had arisen in stationary phase can be studied without confounding effects caused by the occurrence of similar mutations during growth of the population. In two different applications of this strategy, we have studied the reversion to Lac+ in stationary phase of several Lac- mutations in Escherichia coli. Our results indicate that a variety of spontaneous point mutations and deletions, particularly those that are sensitive to the mechanisms of replication slippage (for their generation) and methyl-directed mismatch repair (for their correction), can arise in nondividing populations of cells within a colony. The frequency of their occurrence was also elevated in mutS strains, which are defective in such mismatch repair. These data have relevance to the ongoing debate on adaptive or directed mutations in bacteria.
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Affiliation(s)
- M Reddy
- Centre for Cellular and Molecular Biology, Hyderabad, India
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Akgün E, Zahn J, Baumes S, Brown G, Liang F, Romanienko PJ, Lewis S, Jasin M. Palindrome resolution and recombination in the mammalian germ line. Mol Cell Biol 1997; 17:5559-70. [PMID: 9271431 PMCID: PMC232404 DOI: 10.1128/mcb.17.9.5559] [Citation(s) in RCA: 130] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Genetic instability is promoted by unusual sequence arrangements and DNA structures. Hairpin DNA structures can form from palindromes and from triplet repeats, and they are also intermediates in V(D)J recombination. We have measured the genetic stability of a large palindrome which has the potential to form a one-stranded hairpin or a two-stranded cruciform structure and have analyzed recombinants at the molecular level. A palindrome of 15.3 kb introduced as a transgene was found to be transmitted at a normal Mendelian ratio in mice, in striking contrast to the profound instability of large palindromes in prokaryotic systems. In a significant number of progeny mice, however, the palindromic transgene is rearranged; between 15 and 56% of progeny contain rearrangements. Rearrangements within the palindromic repeat occur both by illegitimate and homologous, reciprocal recombination. Gene conversion within the transgene locus, as quantitated by a novel sperm fluorescence assay, is also elevated. Illegitimate events often take the form of an asymmetric deletion that eliminates the central symmetry of the palindrome. Such asymmetric transgene deletions, including those that maintain one complete half of the palindromic repeat, are stabilized so that they cannot undergo further illegitimate rearrangements, and they also exhibit reduced levels of gene conversion. By contrast, transgene rearrangements that maintain the central symmetry continue to be unstable. Based on the observed events, we propose that one mechanism promoting the instability of the palindrome may involve breaks generated at the hairpin structure by a hairpin-nicking activity, as previously detected in somatic cells. Because mammalian cells are capable of efficiently repairing chromosome breaks through nonhomologous processes, the resealing of such breaks introduces a stabilizing asymmetry at the center of the palindrome. We propose that the ability of mammalian cells to eliminate the perfect symmetry in a palindromic sequence may be an important DNA repair pathway, with implications regarding the metabolism of palindromic repeats, the mutability of quasipalindromic triplet repeats, and the early steps in gene amplification events.
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Affiliation(s)
- E Akgün
- Cell Biology and Genetics Program, Sloan-Kettering Institute and Cornell University Graduate School of Medical Sciences, New York, New York 10021, USA
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Morel P, Cherny D, Ehrlich SD, Cassuto E. Recombination-dependent repair of DNA double-strand breaks with purified proteins from Escherichia coli. J Biol Chem 1997; 272:17091-6. [PMID: 9202026 DOI: 10.1074/jbc.272.27.17091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have developed an in vitro system in which repair of DNA double-strand breaks is performed by purified proteins of Escherichia coli. A segment was deleted from a circular duplex DNA molecule by restriction at two sites. 3' single-stranded overhangs were introduced at both ends of the remaining linear fragment. In a first step, RecA protein catalyzed the formation of a D-loop between one single-stranded tail and a homologous undeleted supercoiled DNA molecule. In a second step, E. coli DNA polymerase II or III used the 3' end in the D-loop as a primer to copy the missing sequences of the linear substrate on one strand of the supercoiled template. Under proper conditions, the integrity of the deleted substrate was restored, as shown by analysis of the products by electrophoresis, restriction, and transformation. In this reaction, DNA synthesis is strictly dependent on recombination, and repair is achieved without formation of a Holliday junction.
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Affiliation(s)
- P Morel
- Institut National de la Recherche Agronomique, Biotechnologies, Génétique Microbienne, 78352 Jouy en Josas Cedex, France
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Reddy M, Gowrishankar J. Identification and characterization of ssb and uup mutants with increased frequency of precise excision of transposon Tn10 derivatives: nucleotide sequence of uup in Escherichia coli. J Bacteriol 1997; 179:2892-9. [PMID: 9139905 PMCID: PMC179051 DOI: 10.1128/jb.179.9.2892-2899.1997] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A Lac+ papillation assay was used to identify mutants (tex) of Escherichia coli that exhibit an increased frequency of precise excision of a lacZ::Tn10dKan insertion. Three tex strains had suffered mutations in the gene (ssb) encoding the essential single-stranded DNA-binding protein SSB, which resulted in the following alterations in the 177-residue protein: G4D; L10F, P24S; and V102M. The phenotypes of these ssb mutants indicated that they were largely unaffected in other functions mediated by SSB, such as DNA replication, recombination, and repair. Strains with multicopy ssb+ exhibited a decreased frequency of Tn10dKan precise excision. Three other tex mutants had insertion mutations in the locus designated uup at 21.75 min on the linkage map. The nucleotide sequence of uup was determined, and the gene was inferred to encode a 625-amino-acid hydrophilic protein that belongs to the superfamily of ABC-domain proteins (with two pairs of the Walker A and B motifs), which are postulated to be involved in coupling ATP hydrolysis with other biological processes. The uup gene product shares extensive homology with the deduced sequences of two proteins of Haemophilus influenzae. The uup gene is also situated immediately upstream of (and is transcribed in the same direction as) the paraquat-inducible SoxRS-regulated pqi-5 gene, two reported promoters for which are situated within the uup coding sequence.
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Affiliation(s)
- M Reddy
- Centre for Cellular & Molecular Biology, Hyderabad, India
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Tran H, Degtyareva N, Gordenin D, Resnick MA. Altered replication and inverted repeats induce mismatch repair-independent recombination between highly diverged DNAs in yeast. Mol Cell Biol 1997; 17:1027-36. [PMID: 9001255 PMCID: PMC231827 DOI: 10.1128/mcb.17.2.1027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Replication, DNA organization, and mismatch repair (MMR) can influence recombination. We examined the effects of altered replication due to a mutation in the polymerase delta gene, long inverted repeats (LIRs) in motifs similar to those in higher eukaryotes, and MMR on intrachromosomal recombination between highly diverged (28%) truncated genes in Saccharomyces cerevisiae. A combination of altered replication and an LIR increased recombination up to 700-fold, while each alone led to a 3- to 20-fold increase. Homeologous recombination was not altered by pms1, msh2, and msh3 mismatch repair mutations. Similar to our previous observations for replication slippage-mediated deletions, there were > or = 5-bp identical runs at the recombination breakpoints. We propose that the dramatic increase in recombination results from enhancement of the effects of altered replication by the LIR, leading to recombinationally active initiating structures. Such interactions predict replication-related, MMR-independent genome changes.
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Affiliation(s)
- H Tran
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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