151
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Roberts J, Park JS. Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr Opin Microbiol 2004; 7:120-5. [PMID: 15063847 DOI: 10.1016/j.mib.2004.02.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mfd is a widely conserved bacterial protein that couples DNA repair with transcription. Mfd recognizes RNA polymerase stalled at a non-coding template site of DNA damage, disrupts the transcription complex to release the transcript and enzyme, and recruits the DNA excision repair machinery to the site. The mechanism of RNA release has been illuminated by the discovery that Mfd causes forward translocation of RNA polymerase, using an ATP-dependent motor that is highly homologous to that of the Holliday branch migration protein RecG.
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Affiliation(s)
- Jeffrey Roberts
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
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152
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Artsimovitch I, Patlan V, Sekine SI, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG. Structural basis for transcription regulation by alarmone ppGpp. Cell 2004; 117:299-310. [PMID: 15109491 DOI: 10.1016/s0092-8674(04)00401-5] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Revised: 02/23/2004] [Accepted: 02/24/2004] [Indexed: 11/19/2022]
Abstract
Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.
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Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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153
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Briggs GS, Mahdi AA, Weller GR, Wen Q, Lloyd RG. Interplay between DNA replication, recombination and repair based on the structure of RecG helicase. Philos Trans R Soc Lond B Biol Sci 2004; 359:49-59. [PMID: 15065656 PMCID: PMC1693295 DOI: 10.1098/rstb.2003.1364] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent studies in Escherichia coli indicate that the interconversion of DNA replication fork and Holliday junction structures underpins chromosome duplication and helps secure faithful transmission of the genome from one generation to the next. It facilitates interplay between DNA replication, recombination and repair, and provides means to rescue replication forks stalled by lesions in or on the template DNA. Insight into how this interconversion may be catalysed has emerged from genetic, biochemical and structural studies of RecG protein, a member of superfamily 2 of DNA and RNA helicases. We describe how a single molecule of RecG might target a branched DNA structure and translocate a single duplex arm to drive branch migration of a Holliday junction, interconvert replication fork and Holliday junction structures and displace the invading strand from a D loop formed during recombination at a DNA end. We present genetic evidence suggesting how the latter activity may provide an efficient pathway for the repair of DNA double-strand breaks that avoids crossing over, thus facilitating chromosome segregation at cell division.
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Affiliation(s)
- Geoffrey S Briggs
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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154
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Loot C, Turlan C, Chandler M. Host processing of branched DNA intermediates is involved in targeted transposition of IS911. Mol Microbiol 2004; 51:385-93. [PMID: 14756780 DOI: 10.1046/j.1365-2958.2003.03850.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A simplified system using bacterial insertion sequence IS911 has been developed to investigate targeted insertion next to DNA sequences resembling IS ends. We show here that these IR-targeted events occur by an unusual mechanism. In the circular IS911 transposition intermediate the two IRs are abutted to form an IR/IR junction. IR-targeted insertion involves transfer of a single end of the junction to the target IR to generate a branched DNA structure. The single-end transfer (SET) intermediate, but not the final insertion product, can be detected in an in vitro reaction. SET intermediates must be processed by the bacterial host to obtain the final insertion products. Sequence analysis of these IR-targeted insertion products and of those obtained in vivo revealed high levels of DNA sequence conversion in which mutations from one IR were transferred to another. These sequence changes cannot be explained by the classic transposition pathway. A model is presented in which the four-way Holliday-like junction created by SET is processed by host-mediated branch migration, resolution, repair and replication. This pathway resembles those described for processing other branched DNA structures such as stalled replication forks.
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Affiliation(s)
- Celine Loot
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS UMR5100, 118 Rte de Narbonne, F31062 Toulouse, France
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155
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Donaldson JR, Courcelle CT, Courcelle J. RuvAB and RecG Are Not Essential for the Recovery of DNA Synthesis Following UV-Induced DNA Damage in Escherichia coli. Genetics 2004. [DOI: 10.1093/genetics/166.4.1631] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Ultraviolet light induces DNA lesions that block the progression of the replication machinery. Several models speculate that the resumption of replication following disruption by UV-induced DNA damage requires regression of the nascent DNA or migration of the replication machinery away from the blocking lesion to allow repair or bypass of the lesion to occur. Both RuvAB and RecG catalyze branch migration of three- and four-stranded DNA junctions in vitro and are proposed to catalyze fork regression in vivo. To examine this possibility, we characterized the recovery of DNA synthesis in ruvAB and recG mutants. We found that in the absence of either RecG or RuvAB, arrested replication forks are maintained and DNA synthesis is resumed with kinetics that are similar to those in wild-type cells. The data presented here indicate that RecG- or RuvAB-catalyzed fork regression is not essential for DNA synthesis to resume following arrest by UV-induced DNA damage in vivo.
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Affiliation(s)
- Janet R Donaldson
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762
| | - Charmain T Courcelle
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762
| | - Justin Courcelle
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762
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156
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Schürer KA, Rudolph C, Ulrich HD, Kramer W. Yeast MPH1 Gene Functions in an Error-Free DNA Damage Bypass Pathway That Requires Genes From Homologous Recombination, but Not From Postreplicative Repair. Genetics 2004. [DOI: 10.1093/genetics/166.4.1673] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Abstract
The MPH1 gene from Saccharomyces cerevisiae, encoding a member of the DEAH family of proteins, had been identified by virtue of the spontaneous mutator phenotype of respective deletion mutants. Genetic analysis suggested that MPH1 functions in a previously uncharacterized DNA repair pathway that protects the cells from damage-induced mutations. We have now analyzed genetic interactions of mph1 with a variety of mutants from different repair systems with respect to spontaneous mutation rates and sensitivities to different DNA-damaging agents. The dependence of the mph1 mutator phenotype on REV3 and REV1 and the synergy with mutations in base and nucleotide excision repair suggest an involvement of MPH1 in error-free bypass of lesions. However, although we observed an unexpected partial suppression of the mph1 mutator phenotype by rad5, genetic interactions with other mutations in postreplicative repair imply that MPH1 does not belong to this pathway. Instead, mutations from the homologous recombination pathway were found to be epistatic to mph1 with respect to both spontaneous mutation rates and damage sensitivities. Determination of spontaneous mitotic recombination rates demonstrated that mph1 mutants are not deficient in homologous recombination. On the contrary, in an sgs1 background we found a pronounced hyperrecombination phenotype. Thus, we propose that MPH1 is involved in a branch of homologous recombination that is specifically dedicated to error-free bypass.
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Affiliation(s)
- K Anke Schürer
- Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, University of Göttingen, D-37077 Göttingen, Germany
| | - Christian Rudolph
- Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, University of Göttingen, D-37077 Göttingen, Germany
| | - Helle D Ulrich
- Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Wilfried Kramer
- Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, University of Göttingen, D-37077 Göttingen, Germany
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157
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Robu ME, Inman RB, Cox MM. Situational repair of replication forks: roles of RecG and RecA proteins. J Biol Chem 2003; 279:10973-81. [PMID: 14701860 DOI: 10.1074/jbc.m312184200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Replication forks often stall or collapse when they encounter a DNA lesion. Fork regression is part of several major paths to the repair of stalled forks, allowing nonmutagenic bypass of the lesion. We have shown previously that Escherichia coli RecA protein can promote extensive regression of a forked DNA substrate that mimics a possible structure of a replication fork stalled at a leading strand lesion. Using electron microscopy and gel electrophoresis, we demonstrate that another protein, E. coli RecG helicase, promotes extensive fork regression in the same system. The RecG-catalyzed fork regression is very efficient and faster than the RecA-promoted reaction (up to 240 bp s(-1)), despite very limited processivity of the RecG protein. The reaction is dependent upon ATP hydrolysis and is stimulated by single-stranded binding protein. The RecA- and RecG-promoted reactions are not synergistic. In fact, RecG functions poorly under the conditions optimal for the RecA reaction, and vice versa. When both RecA and RecG proteins are incubated with the DNA substrate, high RecG concentrations inhibit the RecA protein-promoted fork regression. The very different reaction profiles may reflect a situational application of these proteins to the rescue of stalled replication forks in vivo.
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Affiliation(s)
- Mara E Robu
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706-1544, USA
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158
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Rafferty JB, Bolt EL, Muranova TA, Sedelnikova SE, Leonard P, Pasquo A, Baker PJ, Rice DW, Sharples GJ, Lloyd RG. The Structure of Escherichia coli RusA Endonuclease Reveals a New Holliday Junction DNA Binding Fold. Structure 2003; 11:1557-67. [PMID: 14656440 DOI: 10.1016/j.str.2003.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Holliday junction resolution performed by a variety of structure-specific endonucleases is a key step in DNA recombination and repair. It is believed that all resolvases carry out their reaction chemistries in a similar fashion, utilizing a divalent cation to facilitate the hydrolysis of the phosphodiester backbone of the DNA, but their architecture varies. To date, with the exception of bacteriophage T4 endonuclease VII, each of the known resolvase enzyme structures has been categorized into one of two families: the integrases and the nucleases. We have now determined the structure of the Escherichia coli RusA Holliday junction resolvase, which reveals a fourth structural class for these enzymes. The structure suggests that dimer formation is essential for Mg(2+) cation binding and hence catalysis and that like the other resolvases, RusA distorts its Holliday junction target upon binding. Key residues identified by mutagenesis experiments are well positioned to interact with the DNA.
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Affiliation(s)
- John B Rafferty
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom.
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159
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Abstract
DNA damage encountered during the cellular process of chromosomal replication can disrupt the replication machinery and result in mutagenesis or lethality. The RecA protein of Escherichia coli is essential for survival in this situation: It maintains the integrity of the arrested replication fork and signals the upregulation of over 40 gene products, of which most are required to restore the genomic template and to facilitate the resumption of processive replication. Although RecA was originally discovered as a gene product that was required to change the genetic information during sexual cell cycles, over three decades of research have revealed that it is also the key enzyme required to maintain the genetic information when DNA damage is encountered during replication in asexual cell cycles. In this review, we examine the significant experimental approaches that have led to our current understanding of the RecA-mediated processes that restore replication following encounters with DNA damage.
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Affiliation(s)
- Justin Courcelle
- Department of Biological Sciences, Box GY, Mississippi State University, Mississippi State, Mississippi 39762, USA.
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160
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Makovets S, Powell LM, Titheradge AJB, Blakely GW, Murray NE. Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease? Mol Microbiol 2003; 51:135-47. [PMID: 14651617 DOI: 10.1046/j.1365-2958.2003.03801.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It has been generally accepted that DNA modification protects the chromosome of a bacterium encoding a restriction and modification system. But, when target sequences within the chromosome of one such bacterium (Escherichia coli K-12) are unmodified, the cell does not destroy its own DNA; instead, ClpXP inactivates the nuclease, and restriction is said to be alleviated. Thus, the resident chromosome is recognized as 'self' rather than 'foreign' even in the absence of modification. We now provide evidence that restriction alleviation may be a characteristic of Type I restriction-modification systems, and that it can be achieved by different mechanisms. Our experiments support disassembly of active endonuclease complexes as a potential mechanism. We identify amino acid substitutions in a restriction endonuclease, which impair restriction alleviation in response to treatment with a mutagen, and demonstrate that restriction alleviation serves to protect the chromosome even in the absence of mutagenic treatment. In the absence of efficient restriction alleviation, a Type I restriction enzyme cleaves host DNA and, under these conditions, homologous recombination maintains the integrity of the bacterial chromosome.
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Affiliation(s)
- Svetlana Makovets
- Institute of Cell and Molecular Biology, Darwin Building, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
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161
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Cleary JD, Pearson CE. The contribution of cis-elements to disease-associated repeat instability: clinical and experimental evidence. Cytogenet Genome Res 2003; 100:25-55. [PMID: 14526163 DOI: 10.1159/000072837] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2002] [Accepted: 02/11/2003] [Indexed: 11/19/2022] Open
Abstract
Alterations in the length (instability) of gene-specific microsatellites and minisatellites are associated with at least 35 human diseases. This review will discuss the various cis-elements that contribute to repeat instability, primarily through examination of the most abundant disease-associated repetitive element, trinucleotide repeats. For the purpose of this review, we define cis-elements to include the sequence of the repeat units, the length and purity of the repeat tracts, the sequences flanking the repeat, as well as the surrounding epigenetic environment, including DNA methylation and chromatin structure. Gender-, tissue-, developmental- and locus-specific cis-elements in conjunction with trans-factors may facilitate instability through the processes of DNA replication, repair and/or recombination. Here we review the available human data that supports the involvement of cis-elements in repeat instability with limited reference to model systems. In diverse tissues at different developmental times and at specific loci, repetitive elements display variable levels of instability, suggesting vastly different mechanisms may be responsible for repeat instability amongst the disease loci and between various tissues.
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Affiliation(s)
- J D Cleary
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
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162
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Huertas P, Aguilera A. Cotranscriptionally Formed DNA:RNA Hybrids Mediate Transcription Elongation Impairment and Transcription-Associated Recombination. Mol Cell 2003; 12:711-21. [PMID: 14527416 DOI: 10.1016/j.molcel.2003.08.010] [Citation(s) in RCA: 563] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Genetic instability, a phenomenon relevant for developmentally regulated processes, cancer, and inherited disorders, can be induced by transcription. However, the mechanisms of transcription-associated genetic instability are not yet understood. Analysis of S. cerevisiae mutants of THO/TREX, a conserved eukaryotic protein complex functioning at the interface of transcription and mRNA metabolism, has provided evidence that transcription elongation impairment can cause hyperrecombination. Here we show, using hpr1Delta mutants, that the nascent mRNA can diminish transcription elongation efficiency and promote recombination. If during transcription the nascent mRNA is self-cleaved by a hammerhead ribozyme, the transcription-defect and hyperrecombination phenotypes of hpr1Delta cells are suppressed. Abolishment of hyperrecombination by overexpression of RNase H1 and molecular detection of DNA:RNA hybrids indicate that these are formed cotranscriptionally in hpr1Delta cells. These data support a model to explain the connection between recombination, transcription, and mRNA metabolism and provide a new perspective to understanding transcription-associated recombination.
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Affiliation(s)
- Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avenida Reina, Mercedes 6, 41012 Seville, Spain
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163
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Ahn JS, Whitby MC. The role of the SAP motif in promoting Holliday junction binding and resolution by SpCCE1. J Biol Chem 2003; 278:29121-9. [PMID: 12748193 DOI: 10.1074/jbc.m302314200] [Citation(s) in RCA: 15] [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
Holliday junctions are four-way branched DNA structures that are formed during recombination and by replication fork regression. Their processing depends on helicases that catalyze junction branch migration, and endonucleases that resolve the junction into nicked linear DNAs. Here we have investigated the role of a DNA binding motif called SAP in binding and resolving Holliday junctions by the fission yeast mitochondrial resolvase SpCCE1. Mutation or partial/complete deletion of the SAP motif dramatically impairs the ability of SpCCE1 to resolve Holliday junctions in a heterologous in vivo system. These mutant proteins retain the ability to recognize the junction structure and to distort it upon binding. However, once formed the mutant protein-junction complexes are relatively unstable and dissociate much faster than wild-type complexes. We show that binding stability is necessary for efficient junction resolution, and that this may be due in part to a requirement for maintaining the junction in an open conformation so that it can branch migrate to cleavable sites.
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Affiliation(s)
- Jong Sook Ahn
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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164
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Henry-Mowatt J, Jackson D, Masson JY, Johnson PA, Clements PM, Benson FE, Thompson LH, Takeda S, West SC, Caldecott KW. XRCC3 and Rad51 modulate replication fork progression on damaged vertebrate chromosomes. Mol Cell 2003; 11:1109-17. [PMID: 12718895 DOI: 10.1016/s1097-2765(03)00132-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The mechanisms by which the progression of eukaryotic replication forks is controlled after DNA damage are unclear. We have found that fork progression is slowed by cisplatin or UV treatment in intact vertebrate cells and in replication assays in vitro. Fork slowing is reduced or absent in irs1SF CHO cells and XRCC3(-/-) chicken DT40 cells, indicating that fork slowing is an active process that requires the homologous recombination protein XRCC3. The addition of purified human Rad51C-XRCC3 complex restores fork slowing in permeabilized XRCC3(-/-) cells. Moreover, the requirement for XRCC3 for fork slowing can be circumvented by addition of human Rad51. These data demonstrate that the recombination proteins XRCC3 and Rad51 cooperatively modulate the progression of replication forks on damaged vertebrate chromosomes.
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Affiliation(s)
- Judith Henry-Mowatt
- School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, United Kingdom
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165
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Whitby MC, Osman F, Dixon J. Cleavage of model replication forks by fission yeast Mus81-Eme1 and budding yeast Mus81-Mms4. J Biol Chem 2003; 278:6928-35. [PMID: 12473680 DOI: 10.1074/jbc.m210006200] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The blockage of replication forks can result in the disassembly of the replicative apparatus and reversal of the fork to form a DNA junction that must be processed in order for replication to restart and sister chromatids to segregate at mitosis. Fission yeast Mus81-Eme1 and budding yeast Mus81-Mms4 are endonucleases that have been implicated in the processing of aberrant DNA junctions formed at stalled replication forks. Here we have investigated the activity of purified Mus81-Eme1 and Mus81-Mms4 on substrates that resemble DNA junctions that are expected to form when a replication fork reverses. Both enzymes cleave Holliday junctions and substrates that resemble normal replication forks poorly or not at all. However, forks where the equivalents of either both the leading and lagging strands or just the lagging strand are juxtaposed at the junction point, or where either the leading or lagging strand has been unwound to produce a fork with a single-stranded tail, are cleaved well. Cleavage sites map predominantly between 3 and 6 bp 5' of the junction point. For most substrates the leading strand template is cleaved. The sole exception is a fork with a 5' single-stranded tail, which is cleaved in the lagging strand template.
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Affiliation(s)
- Matthew C Whitby
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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166
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Moore T, McGlynn P, Ngo HP, Sharples GJ, Lloyd RG. The RdgC protein of Escherichia coli binds DNA and counters a toxic effect of RecFOR in strains lacking the replication restart protein PriA. EMBO J 2003; 22:735-45. [PMID: 12554673 PMCID: PMC140733 DOI: 10.1093/emboj/cdg048] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
PriA protein provides a means to load the DnaB replicative helicase at DNA replication fork and D loop structures, and is therefore a key factor in the rescue of stalled or broken forks and subsequent replication restart. We show that the nucleoid-associated RdgC protein binds non-specifically to single-stranded (ss) DNA and double-stranded DNA. It is also essential for growth of a strain lacking PriA, indicating that it might affect replication fork progression or fork rescue. dnaC suppressors of priA overcome this inviability, especially when RecF, RecO or RecR is inactivated, indicating that RdgC avoids or counters a toxic effect of these proteins. Mutations modifying ssDNA-binding (SSB) protein also negate this toxic effect, suggesting that the toxicity reflects inappropriate loading of RecA on SSB-coated ssDNA, leading to excessive or untimely RecA activity. We suggest that binding of RdgC to DNA limits RecA loading, avoiding problems at replication forks that would otherwise require PriA to promote replication restart. Mutations in RNA polymerase also reduce the toxic effect of RecFOR, providing a further link between DNA replication, transcription and repair.
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Affiliation(s)
| | | | | | - Gary J. Sharples
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, University of Durham, Wolfson Research Institute, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
| | - Robert G. Lloyd
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, University of Durham, Wolfson Research Institute, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
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167
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Mahdi AA, Briggs GS, Sharples GJ, Wen Q, Lloyd RG. A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins. EMBO J 2003; 22:724-34. [PMID: 12554672 PMCID: PMC140728 DOI: 10.1093/emboj/cdg043] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RecG protein differs from other helicases analysed to atomic resolution in that it mediates strand separation via translocation on double-stranded (ds) rather than single-stranded (ss) DNA. We describe a highly conserved helical hairpin motif in RecG and show it to be important for helicase activity. It places two arginines (R609 and R630) in opposing positions within the component helices where they are stabilized by a network of hydrogen bonds involving a glutamate from helicase motif VI. We suggest that disruption of this feature, triggered by ATP hydrolysis, moves an adjacent loop structure in the dsDNA-binding channel and that a swinging arm motion of this loop drives translocation. Substitutions that reverse the charge at R609 or R630 reduce DNA unwinding and ATPase activities, and increase dsDNA binding, but do not affect branched DNA binding. Sequences forming the helical hairpin and loop structures are highly conserved in Mfd protein, a transcription-coupled DNA repair factor that also translocates on dsDNA. The possibility of type I restriction enzymes and chromatin-remodelling factors using similar structures to drive translocation on dsDNA is discussed.
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Affiliation(s)
| | | | - Gary J. Sharples
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, Wolfson Research Institute, University of Durham, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
| | | | - Robert G. Lloyd
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, Wolfson Research Institute, University of Durham, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
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168
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Jaktaji RP, Lloyd RG. PriA supports two distinct pathways for replication restart in UV-irradiated Escherichia coli cells. Mol Microbiol 2003; 47:1091-100. [PMID: 12581361 DOI: 10.1046/j.1365-2958.2003.03357.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Escherichia coli PriA protein loads the DnaB replicative helicase at branched DNA structures independently of the replication initiator protein, DnaA, and thereby facilitates assembly of functional replisomes at sites removed from oriC. It is therefore a critical factor in the rescue of replication forks stalled at DNA lesions. It is also a DNA helicase. We describe insertions near the 3' end of priA that interfere with PriA activity. These insertions and the previously described priA300 encoding helicase-defective PriA K230R are shown to be effective suppressors of the DNA repair defect in recG strains, but substantially reduce the ability of ruv mutants to survive DNA damage. The data presented suggest that PriA helicase in conjunction with RecG can promote direct rescue of stalled forks independently of the recombinational pathway promoted by the combined activities of the RuvABC, RecBCD and RecA proteins, which requires only the primosome assembly activity of PriA to load DnaB at D loops. In cells lacking the helicase activity of PriA, we propose that stalled forks can be redirected to the recombination pathway via a Holliday junction intermediate common to both pathways, thus explaining the resistance of these cells to DNA damage.
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Affiliation(s)
- Razieh P Jaktaji
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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169
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Yokoyama H, Kurumizaka H, Ikawa S, Yokoyama S, Shibata T. Holliday junction binding activity of the human Rad51B protein. J Biol Chem 2003; 278:2767-72. [PMID: 12441335 DOI: 10.1074/jbc.m210899200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human Rad51B protein is involved in the recombinational repair of damaged DNA. Chromosomal rearrangements of the Rad51B gene have been found in uterine leiomyoma patients, suggesting that the Rad51B gene suppresses tumorigenesis. In the present study, we found that the purified Rad51B protein bound to single-stranded DNA and double-stranded DNA in the presence of ATP and either Mg(2+) or Mn(2+) and hydrolyzed ATP in a DNA-dependent manner. When the synthetic Holliday junction was present along with the half-cruciform and double-stranded oligonucleotides, the Rad51B protein only bound to the synthetic Holliday junction, which mimics a key intermediate in homologous recombination. In contrast, the human Rad51 protein bound to all three DNA substrates with no obvious preference. Therefore, the Rad51B protein may have a specific function in Holliday junction processing in the homologous recombinational repair pathway in humans.
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Affiliation(s)
- Hiroshi Yokoyama
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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170
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Theobald DL, Mitton-Fry RM, Wuttke DS. Nucleic acid recognition by OB-fold proteins. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2003; 32:115-33. [PMID: 12598368 PMCID: PMC1564333 DOI: 10.1146/annurev.biophys.32.110601.142506] [Citation(s) in RCA: 388] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The OB-fold domain is a compact structural motif frequently used for nucleic acid recognition. Structural comparison of all OB-fold/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these OB-folds. Loops connecting the secondary structural elements in the OB-fold core are extremely variable in length and in functional detail. However, certain features of ligand binding are conserved among OB-fold complexes, including the location of the binding surface, the polarity of the nucleic acid with respect to the OB-fold, and particular nucleic acid-protein interactions commonly used for recognition of single-stranded and unusually structured nucleic acids. Intriguingly, the observation of shared nucleic acid polarity may shed light on the longstanding question concerning OB-fold origins, indicating that it is unlikely that members of this family arose via convergent evolution.
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Affiliation(s)
- Douglas L. Theobald
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215;
| | - Rachel M. Mitton-Fry
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215;
| | - Deborah S. Wuttke
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215;
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171
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Trautinger BW, Lloyd RG. Modulation of DNA repair by mutations flanking the DNA channel through RNA polymerase. EMBO J 2002; 21:6944-53. [PMID: 12486015 PMCID: PMC139083 DOI: 10.1093/emboj/cdf654] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The RuvABC and RecBCD proteins promote rescue of stalled or broken DNA replication forks in Escherichia coli. Strains lacking these proteins cope poorly with DNA damage and have problems with chromosome segregation and cell division. We show how these difficulties are overcome to varying degrees by a sub-class of RNA polymerase mutations selected for their stringent phenotype. Thirty-five mutations were sequenced. All but one change single amino acids in RpoB or RpoC that lie on or near the path taken by DNA through the enzyme, indicating they may affect the stability of transcription complexes. Four mutant enzymes are shown to form unstable open complexes at the lambdacro promoter. At least one may also release stalled complexes or limit their formation, as it reduces the need for reactivation of transcription by GreA or GreB, and for transcription-coupled DNA repair of UV damage by Mfd. The results shed light on the interplay between DNA replication and transcription and suggest ways in which conflicts between these two vital cellular processes are avoided or resolved.
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Affiliation(s)
| | - Robert G. Lloyd
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
Corresponding author e-mail:
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172
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Abstract
The faithful replication of the genome is essential for the survival of all organisms. It is not surprising therefore that numerous mechanisms have evolved to ensure that duplication of the genome occurs with only minimal risk of mutation induction. One mechanism of genome destabilization is replication fork demise, which can occur when a translocating fork meets a lesion or adduct in the template. Indeed, the collapse of replication forks has been suggested to occur in every replicative cell cycle making this a potentially significant problem for all proliferating cells. The RecQ helicases, which are essential for the maintenance of genome stability, are thought to function during DNA replication. In particular, RecQ helicase mutants display replication defects and have phenotypes consistent with an inability to efficiently reinitiate replication following replication fork demise. Here, we review some current models for how replication fork repair might be effected, and discuss potential roles for RecQ helicases in this process.
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Affiliation(s)
- Leonard Wu
- Cancer Research UK Laboratories, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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173
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Abstract
The primary function of bacterial recombination systems is the nonmutagenic repair of stalled or collapsed replication forks. The RecA protein plays a central role in these repair pathways, and its biochemistry must be considered in this context. RecA protein promotes DNA strand exchange, a reaction that contributes to fork regression and DNA end invasion steps. RecA protein activities, especially formation and disassembly of its filaments, affect many additional steps. So far, Escherichia coli RecA appears to be unique among its nearly ubiquitous family of homologous proteins in that it possesses a motorlike activity that can couple the branch movement in DNA strand exchange to ATP hydrolysis. RecA is also a multifunctional protein, serving in different biochemical roles for recombinational processes, SOS induction, and mutagenic lesion bypass. New biochemical and structural information highlights both the similarities and distinctions between RecA and its homologs. Increasingly, those differences can be rationalized in terms of biological function.
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Affiliation(s)
- Shelley L Lusetti
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, USA. ;
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174
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Abstract
DNA repair is crucial to the well-being of all organisms from unicellular life forms to humans. A rich tapestry of mechanistic studies on DNA repair has emerged thanks to the recent discovery of Y-family DNA polymerases. Many Y-family members carry out aberrant DNA synthesis-poor replication accuracy, the favored formation of non-Watson-Crick base pairs, efficient mismatch extension, and most importantly, an ability to replicate through DNA damage. This review is devoted primarily to a discussion of Y-family polymerase members that exhibit error-prone behavior. Roles for these remarkable enzymes occur in widely disparate DNA repair pathways, such as UV-induced mutagenesis, adaptive mutation, avoidance of skin cancer, and induction of somatic cell hypermutation of immunoglobulin genes. Individual polymerases engaged in multiple repair pathways pose challenging questions about their roles in targeting and trafficking. Macromolecular assemblies of replication-repair "factories" could enable a cell to handle the complex logistics governing the rapid migration and exchange of polymerases.
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Affiliation(s)
- Myron F Goodman
- Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratory, University of Southern California, Los Angeles, California 90089-1340, USA.
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175
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McGlynn P, Lloyd RG. Recombinational repair and restart of damaged replication forks. Nat Rev Mol Cell Biol 2002; 3:859-70. [PMID: 12415303 DOI: 10.1038/nrm951] [Citation(s) in RCA: 341] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genome duplication necessarily involves the replication of imperfect DNA templates and, if left to their own devices, replication complexes regularly run into problems. The details of how cells overcome these replicative 'hiccups' are beginning to emerge, revealing a complex interplay between DNA replication, recombination and repair that ensures faithful passage of the genetic material from one generation to the next.
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Affiliation(s)
- Peter McGlynn
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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176
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González-Barrera S, García-Rubio M, Aguilera A. Transcription and double-strand breaks induce similar mitotic recombination events in Saccharomyces cerevisiae. Genetics 2002; 162:603-14. [PMID: 12399375 PMCID: PMC1462300 DOI: 10.1093/genetics/162.2.603] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have made a comparative analysis of double-strand-break (DSB)-induced recombination and spontaneous recombination under low- and high-transcription conditions in yeast. We constructed two different recombination substrates, one for the analysis of intermolecular gene conversions and the other for intramolecular gene conversions and inversions. Such substrates were based on the same leu2-HOr allele fused to the tet promoter and containing a 21-bp HO site. Gene conversions and inversions were differently affected by rad1, rad51, rad52, and rad59 single and double mutations, consistent with the actual view that such events occur by different recombination mechanisms. However, the effect of each mutation on each type of recombination event was the same, whether associated with transcription or induced by the HO-mediated DSB. Both the highly transcribed DNA and the HO-cut sequence acted as recipients of the gene conversion events. These results are consistent with the hypothesis that transcription promotes initiation of recombination along the DNA sequence being transcribed. The similarity between transcription-associated and DSB-induced recombination suggests that transcription promotes DNA breaks.
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177
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Burger A, Raymer J, Bockrath R. DNA damage-processing in E. coli: on-going protein synthesis is required for fixation of UV-induced lethality and mutation. DNA Repair (Amst) 2002; 1:821-31. [PMID: 12531029 DOI: 10.1016/s1568-7864(02)00107-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
UV irradiation of E. coli produces photoproducts in the DNA genome. In consequence, some bacteria lose viability (colony-forming ability) or remain viable as mutant cells. However, the end-points of viability inactivation (lethality) or mutation are determined by cellular processes that act on the UV-damaged DNA. We have investigated the in vivo time course for processes that deal with cyclobutane pyrimidine dimers (CPD) which can be specifically removed by photoreactivation (PR). At different times during post-UV incubation, samples were challenged with PR and assayed for viability or mutation. We used excision-defective E. coli B/r cells and worked under yellow light to avoid background PR. During post-UV incubation (0-100min) in fully supplemented defined medium, inactivation and mutation were initially significantly reversed by PR but the extent of this reversal decreased during continued incubation defining "fixation" of lethality or mutation, respectively. In contrast, if protein synthesis was restricted during the post-UV incubation, no fixation developed. When chloramphenicol was added to inhibit protein synthesis after 30min of supplemented post-UV incubation, at a time sufficient for expression of UV-induced protein(s), fixation of lethality or mutation was still annulled (no change in the effectiveness of PR developed). Lethality fixation did progress when protein synthesis was restricted and the cells were incubated in the presence of puromycin or were either clpP or clpX defective. We discuss these and related results to suggest (1) on-going protein synthesis is required in the fixation process for lethality and mutation to sustain an effective level of a hypothetical protein sensitive to ClpXP proteolysis and (2) this protein plays a critical role in the process leading to exchange between Pol III activity and alternative polymerase activities required as each cell deals with damage in template DNA.
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Affiliation(s)
- Amanda Burger
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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178
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Doe CL, Ahn JS, Dixon J, Whitby MC. Mus81-Eme1 and Rqh1 involvement in processing stalled and collapsed replication forks. J Biol Chem 2002; 277:32753-9. [PMID: 12084712 DOI: 10.1074/jbc.m202120200] [Citation(s) in RCA: 200] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The processing of stalled replication forks and the repair of collapsed replication forks are essential functions in all organisms. In fission yeast DNA junctions at stalled replication forks appear to be processed by either the Rqh1 DNA helicase or Mus81-Eme1 endonuclease. Accordingly, we show that the hypersensitivity to agents that cause replication fork stalling of mus81, eme1, and rqh1 mutants is suppressed by a Holliday junction resolvase (RusA), as is the synthetic lethality of a mus81(-) rqh1(-) double mutant. Recombinant Mus81-Eme1, purified from Escherichia coli, readily cleaves replication fork structures but cleaves synthetic Holliday junctions relatively poorly in vitro. From these data we propose that Mus81-Eme1 can process stalled replication forks before they have regressed to form a Holliday junction. We also implicate Mus81-Eme1 and Rqh1 in the repair of collapsed replication forks. Here Mus81-Eme1 and Rqh1 seem to function on different substrates because RusA can substitute for Mus81-Eme1 but not Rqh1.
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Affiliation(s)
- Claudette L Doe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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179
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Zahradka D, Zahradka K, Petranović M, Dermić D, Brcić-Kostić K. The RuvABC resolvase is indispensable for recombinational repair in sbcB15 mutants of Escherichia coli. J Bacteriol 2002; 184:4141-7. [PMID: 12107131 PMCID: PMC135221 DOI: 10.1128/jb.184.15.4141-4147.2002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RuvABC proteins of Escherichia coli play an important role in the processing of Holliday junctions during homologous recombination and recombinational repair. Mutations in the ruv genes have a moderate effect on recombination and repair in wild-type strains but confer pronounced recombination deficiency and extreme sensitivity to DNA-damaging agents in a recBC sbcBC background. Genetic analysis presented in this work revealed that the (Delta)ruvABC mutation causes an identical DNA repair defect in UV-irradiated recBC sbcBC, sbcBC, and sbcB strains, indicating that the sbcB mutation alone is responsible for the extreme UV sensitivity of recBC sbcBC ruv derivatives. In experiments with gamma irradiation and in conjugational crosses, however, sbcBC (Delta)ruvABC and sbcB (Delta)ruvABC mutants displayed higher recombination proficiency than the recBC sbcBC (Delta)ruvABC strain. The frequency of conjugational recombination observed with the sbcB (Delta)ruvABC strain was quite similar to that of the (Delta)ruvABC single mutant, indicating that the sbcB mutation does not increase the requirement for RuvABC in a recombinational process starting from preexisting DNA ends. The differences between the results obtained in three experimental systems used suggest that in UV-irradiated cells, the RuvABC complex might act in an early stage of recombinational repair. The results of this work are discussed in the context of recent recombination models which propose the participation of RuvABC proteins in the processing of Holliday junctions made from stalled replication forks. We suggest that the mutant SbcB protein stabilizes these junctions and makes their processing highly dependent on RuvABC resolvase.
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Affiliation(s)
- Davor Zahradka
- Department of Molecular Genetics, Ruder Bosković Institute, Zagreb, Croatia.
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180
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Lundin C, Erixon K, Arnaudeau C, Schultz N, Jenssen D, Meuth M, Helleday T. Different roles for nonhomologous end joining and homologous recombination following replication arrest in mammalian cells. Mol Cell Biol 2002; 22:5869-78. [PMID: 12138197 PMCID: PMC133974 DOI: 10.1128/mcb.22.16.5869-5878.2002] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Homologous recombination (HR) and nonhomologous end joining (NHEJ) play overlapping roles in repair of DNA double-strand breaks (DSBs) generated during the S phase of the cell cycle. Here, we characterized the involvement of HR and NHEJ in the rescue of DNA replication forks arrested or slowed by treatment of hamster cells with hydroxyurea or thymidine. We show that the arrest of replication with hydroxyurea generates DNA fragmentation as a consequence of the formation of DSBs at newly replicated DNA. Both HR and NHEJ protected cells from the lethal effects of hydroxyurea, and this agent also increased the frequency of recombination mediated by both homologous and nonhomologous exchanges. Thymidine induced a less stringent arrest of replication and did not generate detectable DSBs. HR alone rescued cells from the lethal effects of thymidine. Furthermore, thymidine increased the frequency of DNA exchange mediated solely by HR in the absence of detectable DSBs. Our data suggest that both NHEJ and HR are involved in repair of arrested replication forks that include a DSB, while HR alone is required for the repair of slowed replication forks in the absence of detectable DSBs.
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Affiliation(s)
- Cecilia Lundin
- Department of Genetic and Cellular Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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181
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Abstract
Chromosomal duplication faces many blocks to replication fork progression that could destabilize the genome and prove fatal if not overcome. Overcoming such blocks requires interplay between DNA replication, recombination and repair. The RecG protein of Escherichia coli promotes rescue of damaged forks by catalysing their unwinding and conversion to Holliday junctions. Subsequent processing of this structure allows repair or bypass of the fork block, enabling replication to resume without recourse to potentially mutagenic translesion synthesis or recombination. Such direct rescue of stalled forks might help safeguard genome integrity in all organisms.
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Affiliation(s)
- Peter McGlynn
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham, UK NG7 2UH.
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182
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Bolt EL, Lloyd RG. Substrate specificity of RusA resolvase reveals the DNA structures targeted by RuvAB and RecG in vivo. Mol Cell 2002; 10:187-98. [PMID: 12150918 DOI: 10.1016/s1097-2765(02)00560-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
RusA endonuclease cleaves Holliday junctions by introducing paired strand incisions 5' to CC dinucleotides. Coordinated catalysis is achieved when both subunits of the homodimer interact simultaneously with cleavage sites located symmetrically. This requirement confers Holliday junction specificity. Uncoupled catalysis occurs when binding interactions are disturbed. Genetic studies indicate that uncoupling occurs rarely in vivo, and DNA cleavage is therefore restricted to Holliday junctions. We exploited the specificity of RusA to identify the DNA substrates targeted by the RuvAB and RecG branch-migration proteins in vivo. We present evidence that replication restart in UV-irradiated cells relies on the processing of stalled replication forks by RecG helicase and of Holliday junctions by the RuvABC resolvasome, and that RuvAB alone may not promote repair.
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Affiliation(s)
- Edward L Bolt
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, United Kingdom
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183
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Abstract
Replacement of the recBCD genes of Escherichia coli with the red recombination genes of bacteriophage lambda results in a strain in which adaptive mutation occurs at an elevated frequency. Like RecBCD-dependent adaptive mutation, Red-mediated adaptive mutation is dependent upon recA and ruvABC functions.
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Affiliation(s)
- Anthony R Poteete
- Department of Molecular Genetics & Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
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184
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Grompone G, Seigneur M, Ehrlich SD, Michel B. Replication fork reversal in DNA polymerase III mutants of Escherichia coli: a role for the beta clamp. Mol Microbiol 2002; 44:1331-9. [PMID: 12028381 DOI: 10.1046/j.1365-2958.2002.02962.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Certain replication mutations lead in Escherichia coli to a specific reaction named replication fork reversal: at blocked forks, annealing of the nascent strands and pairing of the template strands form a four-way junction. RuvABC-catalysed resolution of this Holliday junction causes chromosome double-strand breaks (DSBs) in a recBC context and therefore creates a requirement for the recombination proteins RecBC for viability. In the present work, two mutants were tested for replication fork reversal: a dnaEts mutant and a dnaNts mutant, affected in the alpha (polymerase) and beta (processivity clamp) subunits of DNA polymerase III holoenzyme respectively. In the dnaEts recB strain, RuvABC-dependent DSBs caused by the dnaEts mutation occurred at 37 degrees C or 42 degrees C, indicating the occurrence of replication fork reversal upon partial or complete inactivation of the DNA polymerase alpha subunit. DSB formation was independent of RecA, RecQ and the helicase function of PriA. In the dnaNts recB mutant, RuvABC-dependent DSB caused by the dnaNts mutation occurred only at semi-permissive temperature, 37 degrees C, indicating the occurrence of replication fork reversal in conditions in which the remaining activity of the beta clamp is sufficient for viability. In contrast, the dnaNts mutation did not cause chromosome breakage at 42 degrees C, a temperature at which DnaN is totally inactive and the dnaNts mutant is inviable. We propose that a residual activity of the DNA polymerase III beta clamp is required for replication fork reversal in the dnaNts mutant.
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Affiliation(s)
- Gianfranco Grompone
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, 78352 Jouy en Josas, France
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185
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Seitz EM, Haseltine CA, Kowalczykowski SC. DNA recombination and repair in the archaea. ADVANCES IN APPLIED MICROBIOLOGY 2002; 50:101-69. [PMID: 11677683 DOI: 10.1016/s0065-2164(01)50005-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- E M Seitz
- Sections of Microbiology and of Molecular and Cellular Biology, Center for Genetics and Development, University of California, Davis, Davis, California 95616-8665, USA
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186
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Sharples GJ, Bolt EL, Lloyd RG. RusA proteins from the extreme thermophile Aquifex aeolicus and lactococcal phage r1t resolve Holliday junctions. Mol Microbiol 2002; 44:549-59. [PMID: 11972790 DOI: 10.1046/j.1365-2958.2002.02916.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The RusA protein of Escherichia coli is a DNA structure-specific endonuclease that resolves Holliday junction intermediates formed during DNA replication, recombination and repair by introducing symmetrically paired incisions 5' to CC dinucleotides. It is encoded by the defective prophage DLP12, which raises the possibility that it may be of bacteriophage origin. We show that rusA-like sequences are indeed often associated with prophage sequences in the genomes of several bacterial species. They are also found in many bacteriophages, including Lactococcus lactis phage r1t. However, rusA is also present in the chromosome of the hyperthermophilic bacterium Aquifex aeolicus. In this case, there is no obvious association of rusA with prophage-like sequences. Given the ancient lineage of Aquifex aeolicus, this observation provides the first indication that RusA may be of bacterial origin. The RusA proteins of A. aeolicus and bacteriophage r1t were purified and shown to resolve Holliday junctions. The r1t enzyme also promotes DNA repair in strains lacking the RuvABC resolvase. Both enzymes cleave junctions in a sequence-dependent manner, but the A. aeolicus RusA shows a different sequence preference (3' to TG) from the E. coli protein (5' to CC), and the r1t RusA has relaxed sequence dependence, requiring only a single cytosine.
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Affiliation(s)
- Gary J Sharples
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
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187
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Oakley TJ, Hickson ID. Defending genome integrity during S-phase: putative roles for RecQ helicases and topoisomerase III. DNA Repair (Amst) 2002; 1:175-207. [PMID: 12509252 DOI: 10.1016/s1568-7864(02)00002-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The maintenance of genome stability is important not only for cell viability, but also for the suppression of neoplastic transformation in higher eukaryotes. It has long been recognised that a common feature of cancer cells is genomic instability. Although the so-called three 'Rs' of genome maintenance, DNA replication, recombination and repair, have historically been studied in isolation, a wealth of recent evidence indicates that these processes are intimately interrelated and interdependent. In this article, we will focus on challenges to the maintenance of genome integrity that arise during the S-phase of the cell cycle, and the possible roles that RecQ helicases and topoisomerase III play in the maintenance of genome integrity during the process of DNA replication.
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Affiliation(s)
- Thomas J Oakley
- Cancer Research UK Laboratories, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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188
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Ingleston SM, Dickman MJ, Grasby JA, Hornby DP, Sharples GJ, Lloyd RG. Holliday junction binding and processing by the RuvA protein of Mycoplasma pneumoniae. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1525-33. [PMID: 11874468 DOI: 10.1046/j.1432-1033.2002.02805.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The RuvA, RuvB and RuvC proteins of Escherichia coli act together to process Holliday junctions formed during recombination and DNA repair. RuvA has a well-defined DNA binding surface that is sculptured specifically to accommodate a Holliday junction and allow subsequent loading of RuvB and RuvC. A negatively charged pin projecting from the centre limits binding of linear duplex DNA. The amino-acid sequences forming the pin are highly conserved. However, in certain Mycoplasma and Ureaplasma species the structure is extended by four amino acids and two acidic residues forming a crucial charge barrier are missing. We investigated the significance of these differences by analysing RuvA from Mycoplasma pneumoniae. Gel retardation and surface plasmon resonance assays revealed that this protein binds Holliday junctions and other branched DNA structures in a manner similar to E. coli RuvA. Significantly, it binds duplex DNA more readily. However it does not support branch migration mediated by E. coli RuvB and when bound to junction DNA is unable to provide a platform for stable binding of E. coli RuvC. It also fails to restore radiation resistance to an E. coli ruvA mutant. The data presented suggest that the modified pin region retains the ability to promote junction-specific DNA binding, but acts as a physical obstacle to linear duplex DNA rather than as a charge barrier. They also indicate that such an obstacle may interfere with the binding of a resolvase. Mycoplasma species may therefore process Holliday junctions via uncoupled branch migration and resolution reactions.
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Affiliation(s)
- Stuart M Ingleston
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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189
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Boán F, Rodríguez JM, Mouriño S, Blanco MG, Viñas A, Sánchez L, Gómez-Márquez J. Recombination analysis of the human minisatellite MsH42 suggests the existence of two distinct pathways for initiation and resolution of recombination at MsH42 in rat testes nuclear extracts. Biochemistry 2002; 41:2166-76. [PMID: 11841207 DOI: 10.1021/bi015780i] [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: 11/28/2022]
Abstract
We have previously described a GC-rich human minisatellite, termed MsH42, which exists in two allelic forms, long and short. Here, we have identified a third allele of medium length and localized the MsH42 locus in the chromosome 15q25.1 inside an intron belonging to a gene of unknown function. The recombinogenic potential of the three alleles was assayed in vitro incubating pBR322-based constructs containing two copies of the minisatellite MsH42 with its flanking sequences, in the presence of rat testes nuclear extracts. This assay system was configured to monitor only reciprocal exchange type events and not gene conversion. All MsH42 allelic sequences enhanced intramolecular homologous recombination promoting high rates (approximately 76%) of equal crossover, the long allele showing the highest recombinogenic activity. Removal of the MsH42 long allele flanking sequences, which are identical in the three alleles, provoked a decrease in the enhancement of recombination and in the frequency of equal crossovers, suggesting that these sequences are important for the recombinogenic activity and for the correct pairing between homologous sequences. The occurrence of some complex recombination events within the minisatellite MsH42 suggests the existence of processes related to polymerase slippage and unwinding with reinvasion during the repair synthesis. Our findings point toward the existence of two distinct biochemical pathways for initiation and resolution of recombination at the minisatellite MsH42. Finally, the in vitro recombination system employed in this study could provide an approach to dissect processes of repetitive DNA instability and recombination.
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Affiliation(s)
- Francisco Boán
- Departamento de Bioquímica y Biología Molecular, Facultad de Biología, Universidad de Santiago, 15782 Santiago de Compostela, A Coruña, Galicia, Spain
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190
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Olavarrieta L, Martínez-Robles ML, Sogo JM, Stasiak A, Hernández P, Krimer DB, Schvartzman JB. Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucleic Acids Res 2002; 30:656-66. [PMID: 11809877 PMCID: PMC100290 DOI: 10.1093/nar/30.3.656] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To study the structure of partially replicated plasmids, we cloned the Escherichia coli polar replication terminator TerE in its active orientation at different locations in the ColE1 vector pBR18. The resulting plasmids, pBR18-TerE@StyI and pBR18-TerE@EcoRI, were analyzed by neutral/neutral two-dimensional agarose gel electrophoresis and electron microscopy. Replication forks stop at the Ter-TUS complex, leading to the accumulation of specific replication intermediates with a mass 1.26 times the mass of non-replicating plasmids for pBR18-TerE@StyI and 1.57 times for pBR18-TerE@EcoRI. The number of knotted bubbles detected after digestion with ScaI and the number and electrophoretic mobility of undigested partially replicated topoisomers reflect the changes in plasmid topology that occur in DNA molecules replicated to different extents. Exposure to increasing concentrations of chloroquine or ethidium bromide revealed that partially replicated topoisomers (CCCRIs) do not sustain positive supercoiling as efficiently as their non-replicating counterparts. It was suggested that this occurs because in partially replicated plasmids a positive DeltaLk is absorbed by regression of the replication fork. Indeed, we showed by electron microscopy that, at least in the presence of chloroquine, some of the CCCRIs of pBR18-Ter@StyI formed Holliday-like junction structures characteristic of reversed forks. However, not all the positive supercoiling was absorbed by fork reversal in the presence of high concentrations of ethidium bromide.
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Affiliation(s)
- L Olavarrieta
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain
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191
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Abstract
Transcription is a central aspect of DNA metabolism that takes place on the same substrate as replication, repair and recombination. Not surprisingly, therefore, there is a physical and functional connection between these processes. In recent years, transcription has proven to be a relevant player in the maintenance of genome integrity and in the induction of genetic instability and diversity. The aim of this review is to provide an integrative view on how transcription can control different aspects of genomic integrity, by exploring different mechanisms that might be responsible for transcription-associated mutation (TAM) and transcription-associated recombination (TAR).
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Affiliation(s)
- Andrés Aguilera
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain.
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192
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Rangarajan S, Woodgate R, Goodman MF. Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins. Mol Microbiol 2002; 43:617-28. [PMID: 11929519 DOI: 10.1046/j.1365-2958.2002.02747.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, UV-irradiated cells resume DNA synthesis after a transient inhibition by a process called replication restart. To elucidate the role of several key proteins involved in this process, we have analysed the time dependence of replication restart in strains carrying a combination of mutations in lexA, recA, polB (pol II), umuDC (pol V), priA, dnaC, recF, recO or recR. We find that both pol II and the origin-independent primosome-assembling function of PriA are essential for the immediate recovery of DNA synthesis after UV irradiation. In their absence, translesion replication or 'replication readthrough' occurs approximately 50 min after UV and is pol V-dependent. In a wild-type, lexA+ background, mutations in recF, recO or recR block both pathways. Similar results were obtained with a lexA(Def) recF strain. However, lexA(Def) recO or lexA(Def) recR strains, although unable to facilitate PriA-pol II-dependent restart, were able to perform pol V-dependent readthrough. The defects in restart attributed to mutations in recF, recO or recR were suppressed in a recA730 lexA(Def) strain expressing constitutively activated RecA (RecA*). Our data suggest that in a wild-type background, RecF, O and R are important for the induction of the SOS response and the formation of RecA*-dependent recombination intermediates necessary for PriA/Pol II-dependent replication restart. In con-trast, only RecF is required for the activation of RecA that leads to the formation of pol V (UmuD'2C) and facilitates replication readthrough.
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Affiliation(s)
- Savithri Rangarajan
- Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089-1340, USA
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193
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Gregg AV, McGlynn P, Jaktaji RP, Lloyd RG. Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities. Mol Cell 2002; 9:241-51. [PMID: 11864599 DOI: 10.1016/s1097-2765(02)00455-0] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The PriA protein of Escherichia coli plays a key role in the rescue of replication forks stalled on the template DNA. One attractive model of rescue relies on homologous recombination to establish a new fork via PriA-mediated loading of the DnaB replicative helicase at D loop intermediates. We provide genetic and biochemical evidence that PriA helicase activity can also rescue a stalled fork by an alternative mechanism that requires manipulation of the fork before loading of DnaB on the lagging strand template. This direct rescue depends on RecG, which unwinds forks and Holliday junctions and interconverts these structures. The combined action of PriA and RecG helicase activities may thus avoid the potential dangers of rescue pathways involving fork breakage and recombination.
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Affiliation(s)
- Amanda V Gregg
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, United Kingdom
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194
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Gong L, Takayama K, Kjelleberg S. Role of spoT-dependent ppGpp accumulation in the survival of light-exposed starved bacteria. MICROBIOLOGY (READING, ENGLAND) 2002; 148:559-570. [PMID: 11832519 DOI: 10.1099/00221287-148-2-559] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In bacteria, cytoplasmic levels of the effector nucleotide ppGpp are regulated in response to changes in growth conditions. This study describes the involvement of SpoT-mediated ppGpp accumulation in the survival of light-exposed bacteria during fatty acid starvation. In contrast to isogenic wild-type strains and relA mutants, the 'Vibrio angustum' S14 spoT and Escherichia coli relA spoT mutants displayed significant losses in viability in response to cerulenin-induced fatty acid starvation under cool-white fluorescent light. However, when starvation experiments were performed in complete darkness, or under light filtered through a UV-resistant perspex sheet, only a minor decline in viability was observed for the wild-type and mutant strains. This finding indicated that the lethal effect was mediated by weak UV emission. In contrast to the E. coli relA spoT mutant, which lacks ppGpp, the 'V. angustum' S14 spoT mutant exhibited higher ppGpp levels and lower RNA synthesis rates during fatty acid starvation, features that might be correlated with its lethality. In agreement with this finding, fatty acid starvation lethality also occurred upon induction of ppGpp overaccumulation in E. coli. These data suggest that the precise regulation of ppGpp levels in the stressed cell is crucial, and that both the absence and the overaccumulation of ppGpp impair fatty acid starvation survival of light-exposed cells. Moreover, the UV-induced lethal effect during fatty acid starvation was also observed for E. coli strains mutated in rpoS and dps, which, in the wild-type, are regulated directly or indirectly by ppGpp, respectively. The restoration of viability of fatty-acid-starved spoT mutant cells through the addition of exogenous catalase suggested that the observed light-dependent lethal effect was, at least in part, caused by UV-imposed oxidative stress. Based on these results, it is proposed that fatty acid starvation adaptation of light-exposed bacterial cells depends on the development of resistance to UV-induced oxidative stress. This stress resistance was found to require appropriate ppGpp levels, ppGpp-induced RpoS expression and, hence, upregulation of RpoS-regulated stress-defending genes, such as dps.
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Affiliation(s)
- Lan Gong
- School of Microbiology and Immunology, The University of New South Wales, Sydney 2052, Australia1
| | - Kathy Takayama
- School of Microbiology and Immunology, The University of New South Wales, Sydney 2052, Australia1
| | - Staffan Kjelleberg
- School of Microbiology and Immunology, The University of New South Wales, Sydney 2052, Australia1
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195
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Abstract
It has recently become clear that the recombinational repair of stalled replication forks is the primary function of homologous recombination systems in bacteria. In spite of the rapid progress in many related lines of inquiry that have converged to support this view, much remains to be done. This review focuses on several key gaps in understanding. Insufficient data currently exists on: (a) the levels and types of DNA damage present as a function of growth conditions, (b) which types of damage and other barriers actually halt replication, (c) the structures of the stalled/collapsed replication forks, (d) the number of recombinational repair paths available and their mechanistic details, (e) the enzymology of some of the key reactions required for repair, (f) the role of certain recombination proteins that have not yet been studied, and (g) the molecular origin of certain in vivo observations associated with recombinational DNA repair during the SOS response. The current status of each of these topics is reviewed.
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Affiliation(s)
- M M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.
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196
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Dillingham MS, Wigley DB, Webb MR. Direct measurement of single-stranded DNA translocation by PcrA helicase using the fluorescent base analogue 2-aminopurine. Biochemistry 2002; 41:643-51. [PMID: 11781105 DOI: 10.1021/bi011137k] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Use of the fluorescent base analogue 2-aminopurine has provided a direct demonstration of the translocation of PcrA helicase toward the 5'-end of single-stranded DNA. Single 2-aminopurine bases are introduced into otherwise standard oligonucleotides and produce a fluorescence signal when PcrA reaches their position. We demonstrate that random binding of PcrA to ssDNA is followed by translocation in an ATP-dependent manner toward the 5'-terminus at 80 bases per second at 20 degrees C. The data also provide information on the kinetics of ssDNA binding to the helicase and of the protein dissociation from the 5'-end of ssDNA. A full kinetic model is presented for ATP-dependent DNA translocation by PcrA helicase.
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Affiliation(s)
- Mark S Dillingham
- Imperial Cancer Research Fund, Clare Hall Laboratories, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3LD, UK
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197
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Crowley DJ, Courcelle J. Answering the Call: Coping with DNA Damage at the Most Inopportune Time. J Biomed Biotechnol 2002; 2:66-74. [PMID: 12488586 PMCID: PMC153787 DOI: 10.1155/s1110724302202016] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2002] [Accepted: 02/20/2002] [Indexed: 12/02/2022] Open
Abstract
DNA damage incurred during the process of chromosomal replication has a particularly high possibility of resulting in mutagenesis or lethality for the cell. The SOS response of Escherichia coli appears to be well adapted for this particular situation and involves the coordinated up-regulation of genes whose products center upon the tasks of maintaining the integrity of the replication fork when it encounters DNA damage, delaying the replication process (a DNA damage checkpoint), repairing the DNA lesions or allowing replication to occur over these DNA lesions, and then restoring processive replication before the SOS response itself is turned off. Recent advances in the fields of genomics and biochemistry has given a much more comprehensive picture of the timing and coordination of events which allow cells to deal with potentially lethal or mutagenic DNA lesions at the time of chromosomal replication.
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Affiliation(s)
- David J. Crowley
- Biology Department, Mercer University, 1400 Coleman Avenue, Macon, GA 31207, USA
| | - Justin Courcelle
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS 39762, USA
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198
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Bork JM, Cox MM, Inman RB. The RecOR proteins modulate RecA protein function at 5' ends of single-stranded DNA. EMBO J 2001; 20:7313-22. [PMID: 11743007 PMCID: PMC125792 DOI: 10.1093/emboj/20.24.7313] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Escherichia coli RecF, RecO and RecR pro teins have previously been implicated in bacterial recombinational DNA repair at DNA gaps. The RecOR-facilitated binding of RecA protein to single-stranded DNA (ssDNA) that is bound by single-stranded DNA-binding protein (SSB) is much faster if the ssDNA is linear, suggesting that a DNA end (rather than a gap) facilitates binding. In addition, the RecOR complex facilitates RecA protein-mediated D-loop formation at the 5' ends of linear ssDNAs. RecR protein remains associated with the RecA filament and its continued presence is required to prevent filament disassembly. RecF protein competes with RecO protein for RecR protein association and its addition destabilizes RecAOR filaments. An enhanced function of the RecO and RecR proteins can thus be seen in vitro at the 5' ends of linear ssDNA that is not as evident in DNA gaps. This function is countered by the RecF/RecO competition for association with the RecR protein.
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Affiliation(s)
- Julie M. Bork
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
Present address: Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, 5 Research Court, Rockville, MD 20850, USA Corresponding author e-mail:
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
Present address: Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, 5 Research Court, Rockville, MD 20850, USA Corresponding author e-mail:
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199
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Zahradka K, Zahradka D, Petranović M. Loss of lambda prophage recombinogenicity in UV-irradiated Escherichia coli: the role of host genes ruvA, ruvB, ruvC, and recG. Res Microbiol 2001; 152:873-81. [PMID: 11766962 DOI: 10.1016/s0923-2508(01)01270-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Earlier studies have revealed a radiation-induced process leading to the loss of lambda prophage recombinogenicity. The process takes place in UV-irradiated Escherichia coli cells, and renders the prophage incapable of site-specific recombination with the host chromosome, and of general recombination with an infecting homologous phage. It was found that the inhibition of prophage recombinogenicity depends on functional RecBCD enzyme of E. coli. In this work, the role of ruvABC and recG genes in the inhibitory process was assessed. The products of these genes are known to act at the last step of homologous recombination and recombinational DNA repair by catalyzing the resolution of recombination intermediates (the Holliday junctions). Irradiated prophage retained its ability to recombine in ruvA, ruvB, ruvC, and recG mutants. These results suggest that in addition to RecBCD enzyme, RuvABC and RecG proteins are also involved in the inhibition of prophage recombinogenicity. We infer that RuvABC and RecG act in this process before RecBCD, probably by processing the Holliday junctions formed upon replication arrest, and thereby providing double-stranded DNA breaks as substrate for RecBCD-mediated recombinational repair of UV-damaged bacterial chromosome.
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Affiliation(s)
- K Zahradka
- Department of Molecular Genetics, Ruder Bosković Institute, Zagreb, Croatia.
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200
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Cromie GA, Connelly JC, Leach DR. Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans. Mol Cell 2001; 8:1163-74. [PMID: 11779493 DOI: 10.1016/s1097-2765(01)00419-1] [Citation(s) in RCA: 235] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The recombination mechanisms that deal with double-strand breaks in organisms as diverse as phage, bacteria, yeast, and humans are remarkably conserved. We discuss conservation in the biochemical pathways required to recombine DNA ends and in the structure of the DNA products. In addition, we highlight that two fundamentally distinct broken DNA substrates exist and describe how they are repaired differently by recombination. Finally, we discuss the need to coordinate recombinational repair with cell division through DNA damage response pathways.
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Affiliation(s)
- G A Cromie
- Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, United Kingdom
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