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Wald J, Marlovits TC. Holliday junction branch migration driven by AAA+ ATPase motors. Curr Opin Struct Biol 2023; 82:102650. [PMID: 37604043 DOI: 10.1016/j.sbi.2023.102650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 08/23/2023]
Abstract
Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates an ATP-dependent movement of the Holliday junction (branch migration). Although the RuvAB complex served as a paradigm for the processing of the Holliday junction, due to technical limitations the detailed structure and underlying mechanism of the RuvAB branch migration complex has until now remained unclear. Recently, structures of a reconstituted RuvAB complex actively-processing a Holliday junction were resolved using time-resolved cryo-electron microscopy. These structures showed distinct conformational states at different stages of the migration process. These structures made it possible to propose an integrated model for RuvAB Holliday junction branch migration. Furthermore, they revealed unexpected insights into the highly coordinated and regulated mechanisms of the nucleotide cycle powering substrate translocation in the hexameric AAA+ RuvB ATPase. Here, we review these latest advances and describe areas for future research.
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Affiliation(s)
- Jiri Wald
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany; Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestraße 85, 22607 Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas C Marlovits
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany; Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestraße 85, 22607 Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany.
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2
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Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.
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Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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3
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Bandyopadhyay D, Mishra PP. Revealing the DNA Unwinding Activity and Mechanism of Fork Reversal by RecG While Exposed to Variants of Stalled Replication-fork at Single-Molecular Resolution. J Mol Biol 2022; 434:167822. [PMID: 36108776 DOI: 10.1016/j.jmb.2022.167822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]
Abstract
RecG, belonging to the category of Superfamily-2 plays a vital role in rescuing different kinds of stalled fork. The elemental mechanism of the helicase activity of RecG with several non-homologous stalled fork structures resembling intermediates formed during the process of DNA repair has been investigated in the present study to capture the dynamic stages of genetic rearrangement. The functional characterization has been exemplified through quantifying the response of the substrate in terms of their molecular heterogeneity and dynamical response by employing single-molecule fluorescence methods. An elevated processivity of RecG is observed for the stalled fork where progression of lagging daughter strand is ahead as compared to that of the leading strand. Through precise alteration of its function in terms of unwinding, depending upon the substrate DNA, RecG catalyzes the formation of Holliday junction from a stalled fork DNA. RecG is found to adopt an asymmetric mode of locomotion to unwind the lagging daughter strand for facilitating formation of Holliday junction that acts as a suitable intermediate for recombinational repair pathway. Our results emphasize the mechanism adopted by RecG during its 'sliding back' mode along the lagging daughter strand to be 'active translocation and passive unwinding'. This also provide clues as to how this helicase decides and controls the mode of translocation along the DNA to unwind.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India. https://twitter.com/DebolinaBandyo2
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India.
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4
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The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ. PLoS Genet 2021; 17:e1009972. [PMID: 34936656 PMCID: PMC8735627 DOI: 10.1371/journal.pgen.1009972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/06/2022] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
The RarA protein, homologous to human WRNIP1 and yeast MgsA, is a AAA+ ATPase and one of the most highly conserved DNA repair proteins. With an apparent role in the repair of stalled or collapsed replication forks, the molecular function of this protein family remains obscure. Here, we demonstrate that RarA acts in late stages of recombinational DNA repair of post-replication gaps. A deletion of most of the rarA gene, when paired with a deletion of ruvB or ruvC, produces a growth defect, a strong synergistic increase in sensitivity to DNA damaging agents, cell elongation, and an increase in SOS induction. Except for SOS induction, these effects are all suppressed by inactivating recF, recO, or recJ, indicating that RarA, along with RuvB, acts downstream of RecA. SOS induction increases dramatically in a rarA ruvB recF/O triple mutant, suggesting the generation of large amounts of unrepaired ssDNA. The rarA ruvB defects are not suppressed (and in fact slightly increased) by recB inactivation, suggesting RarA acts primarily downstream of RecA in post-replication gaps rather than in double strand break repair. Inactivating rarA, ruvB and recG together is synthetically lethal, an outcome again suppressed by inactivation of recF, recO, or recJ. A rarA ruvB recQ triple deletion mutant is also inviable. Together, the results suggest the existence of multiple pathways, perhaps overlapping, for the resolution or reversal of recombination intermediates created by RecA protein in post-replication gaps within the broader RecF pathway. One of these paths involves RarA.
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5
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Hu Y, He Y, Lin Z. Biochemical and structural characterization of the Holliday junction resolvase RuvC from Pseudomonas aeruginosa. Biochem Biophys Res Commun 2020; 525:265-271. [PMID: 32085896 DOI: 10.1016/j.bbrc.2020.02.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/19/2022]
Abstract
The Holliday junction, a four-way DNA structure, is an important intermediate of homologous recombination. Proper Holliday junction resolution is critical to complete the recombination process. In most bacterial cells, the Holliday junction cleavage is mainly performed by a specific endonuclease RuvC. Here, we describe the biochemical properties and the crystal structure of RuvC from an opportunistic pathogen, Pseudomonas aeruginosa (PaRuvC). PaRuvC specifically binds to the Holliday junction DNA and preferentially cleaves it at the consensus 5'-TTC-3'. PaRuvC uses Mg2+ as the preferred divalent metal cofactor for Holliday junction cleavage and its optimum pH is 8.0-9.0. Elevated temperatures (37-60 °C) boost the catalytic activity, but temperatures higher than 53 °C reduce the protein stability. The crystal structure of PaRuvC determined at 2.4 Å and mutagenesis analysis reveal key residues involved in the dimer formation, substrate binding and catalysis. Our results are expected to provide useful information to combat antibiotic resistance of Pseudomonas aeruginosa by targeting its homologous recombination system.
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Affiliation(s)
- Yi Hu
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Yuhua He
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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6
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Zhou R, Yang O, Déclais AC, Jin H, Gwon GH, Freeman ADJ, Cho Y, Lilley DMJ, Ha T. Junction resolving enzymes use multivalency to keep the Holliday junction dynamic. Nat Chem Biol 2019; 15:269-275. [PMID: 30664685 PMCID: PMC6377835 DOI: 10.1038/s41589-018-0209-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 11/30/2018] [Indexed: 11/21/2022]
Abstract
Holliday junction (HJ) resolution by resolving enzymes is essential for chromosome segregation and recombination-mediated DNA repair. HJs undergo two types of structural dynamics that determine the outcome of recombination: conformer exchange between two isoforms and branch migration. However, it is unknown how the preferred branch point and conformer are achieved between enzyme binding and HJ resolution given the extensive binding interactions seen in static crystal structures. Single-molecule fluorescence resonance energy transfer analysis of resolving enzymes from bacteriophages (T7 endonuclease I), bacteria (RuvC), fungi (GEN1) and humans (hMus81-Eme1) showed that both types of HJ dynamics still occur after enzyme binding. These dimeric enzymes use their multivalent interactions to achieve this, going through a partially dissociated intermediate in which the HJ undergoes nearly unencumbered dynamics. This evolutionarily conserved property of HJ resolving enzymes provides previously unappreciated insight on how junction resolution, conformer exchange and branch migration may be coordinated.
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Affiliation(s)
- Ruobo Zhou
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, School of Life Sciences, The University of Dundee, Dundee, UK
| | - Hyeonseok Jin
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Gwang Hyeon Gwon
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Alasdair D J Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, School of Life Sciences, The University of Dundee, Dundee, UK
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, School of Life Sciences, The University of Dundee, Dundee, UK
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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7
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Gupta S, Yeeles JTP, Marians KJ. Regression of replication forks stalled by leading-strand template damage: I. Both RecG and RuvAB catalyze regression, but RuvC cleaves the holliday junctions formed by RecG preferentially. J Biol Chem 2014; 289:28376-87. [PMID: 25138216 DOI: 10.1074/jbc.m114.587881] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The orderly progression of replication forks formed at the origin of replication in Escherichia coli is challenged by encounters with template damage, slow moving RNA polymerases, and frozen DNA-protein complexes that stall the fork. These stalled forks are foci for genomic instability and must be reactivated. Many models of replication fork reactivation invoke nascent strand regression as an intermediate in the processing of the stalled fork. We have investigated the replication fork regression activity of RecG and RuvAB, two proteins commonly thought to be involved in the process, using a reconstituted DNA replication system where the replisome is stalled by collision with leading-strand template damage. We find that both RecG and RuvAB can regress the stalled fork in the presence of the replisome and SSB; however, RuvAB generates a completely unwound product consisting of the paired nascent leading and lagging strands, whereas RuvC cleaves the Holliday junction generated by RecG-catalyzed fork regression. We also find that RecG stimulates RuvAB-catalyzed regression, presumably because it is more efficient at generating the initial Holliday junction from the stalled fork.
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Affiliation(s)
- Sankalp Gupta
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Joseph T P Yeeles
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kenneth J Marians
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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8
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Abstract
Homologous recombination is an ubiquitous process that shapes genomes and repairs DNA damage. The reaction is classically divided into three phases: presynaptic, synaptic, and postsynaptic. In Escherichia coli, the presynaptic phase involves either RecBCD or RecFOR proteins, which act on DNA double-stranded ends and DNA single-stranded gaps, respectively; the central synaptic steps are catalyzed by the ubiquitous DNA-binding protein RecA; and the postsynaptic phase involves either RuvABC or RecG proteins, which catalyze branch-migration and, in the case of RuvABC, the cleavage of Holliday junctions. Here, we review the biochemical properties of these molecular machines and analyze how, in light of these properties, the phenotypes of null mutants allow us to define their biological function(s). The consequences of point mutations on the biochemical properties of recombination enzymes and on cell phenotypes help refine the molecular mechanisms of action and the biological roles of recombination proteins. Given the high level of conservation of key proteins like RecA and the conservation of the principles of action of all recombination proteins, the deep knowledge acquired during decades of studies of homologous recombination in bacteria is the foundation of our present understanding of the processes that govern genome stability and evolution in all living organisms.
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Hong Y, Chu M, Li Y, Ni J, Sheng D, Hou G, She Q, Shen Y. Dissection of the functional domains of an archaeal Holliday junction helicase. DNA Repair (Amst) 2011; 11:102-11. [PMID: 22062475 DOI: 10.1016/j.dnarep.2011.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Helicases and nucleases form complexes that play very important roles in DNA repair pathways some of which interact with each other at Holliday junctions. In this study, we present in vitro and in vivo analysis of Hjm and its interaction with Hjc in Sulfolobus. In vitro studies employed Hjm from the hyperthermophilic archaeon Sulfolobus tokodaii (StoHjm) and its truncated derivatives, and characterization of the StoHjm proteins revealed that the N-terminal module (residues 1-431) alone was capable of ATP hydrolysis and DNA binding, while the C-terminal one (residues 415-704) was responsible for regulating the helicase activity. The region involved in StoHjm-StoHjc (Hjc from S. tokodaii) interaction was identified as part of domain II, domain III (Winged Helix motif), and domain IV (residues 366-645) for StoHjm. We present evidence supporting that StoHjc regulates the helicase activity of StoHjm by inducing conformation change of the enzyme. Furthermore, StoHjm is able to prevent the formation of Hjc/HJ high complex, suggesting a regulation mechanism of Hjm to the activity of Hjc. We show that Hjm is essential for cell viability using recently developed genetic system and mutant propagation assay, suggesting that Hjm/Hjc mediated resolution of stalled replication forks is of crucial importance in archaea. A tentative pathway with which Hjm/Hjc interaction could have occurred at stalled replication forks is discussed.
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Affiliation(s)
- Ye Hong
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, PR China
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10
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Bichara M, Meier M, Wagner J, Cordonnier A, Lambert IB. Postreplication repair mechanisms in the presence of DNA adducts in Escherichia coli. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2011; 727:104-22. [DOI: 10.1016/j.mrrev.2011.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 04/25/2011] [Accepted: 04/26/2011] [Indexed: 02/02/2023]
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Morita R, Nakane S, Shimada A, Inoue M, Iino H, Wakamatsu T, Fukui K, Nakagawa N, Masui R, Kuramitsu S. Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems. J Nucleic Acids 2010; 2010:179594. [PMID: 20981145 PMCID: PMC2957137 DOI: 10.4061/2010/179594] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/27/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is subjected to many endogenous and exogenous damages. All organisms have developed a complex network of DNA repair mechanisms. A variety of different DNA repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. Recent studies of the fundamental mechanisms for DNA repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as functional interactions between proteins involved in repair pathways. In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly in Thermus thermophilus HB8.
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Affiliation(s)
- Rihito Morita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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12
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Fonville NC, Bates D, Hastings PJ, Hanawalt PC, Rosenberg SM. Role of RecA and the SOS response in thymineless death in Escherichia coli. PLoS Genet 2010; 6:e1000865. [PMID: 20221259 PMCID: PMC2832678 DOI: 10.1371/journal.pgen.1000865] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 01/29/2010] [Indexed: 01/08/2023] Open
Abstract
Thymineless death (TLD) is a classic and enigmatic phenomenon, documented in bacterial, yeast, and human cells, whereby cells lose viability rapidly when deprived of thymine. Despite its being the essential mode of action of important chemotherapeutic agents, and despite having been studied extensively for decades, the basic mechanisms of TLD have remained elusive. In Escherichia coli, several proteins involved in homologous recombination (HR) are required for TLD, however, surprisingly, RecA, the central HR protein and activator of the SOS DNA-damage response was reported not to be. We demonstrate that RecA and the SOS response are required for a substantial fraction of TLD. We show that some of the Rec proteins implicated previously promote TLD via facilitating activation of the SOS response and that, of the roughly 40 proteins upregulated by SOS, SulA, an SOS-inducible inhibitor of cell division, accounts for most or all of how SOS causes TLD. The data imply that much of TLD results from an irreversible cell-cycle checkpoint due to blocked cell division. FISH analyses of the DNA in cells undergoing TLD reveal blocked replication and apparent DNA loss with the region near the replication origin underrepresented initially and the region near the terminus lost later. Models implicating formation of single-strand DNA at blocked replication forks, a SulA-blocked cell cycle, and RecQ/RecJ-catalyzed DNA degradation and HR are discussed. The data predict the importance of DNA damage-response and HR networks to TLD and chemotherapy resistance in humans.
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Affiliation(s)
- Natalie C. Fonville
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Graduate Program in Cellular and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Graduate Program in Cellular and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - P. J. Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Philip C. Hanawalt
- Department of Biological Sciences, Stanford University, Stanford, California, United States of America
| | - Susan M. Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Graduate Program in Cellular and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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13
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RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box. J Bacteriol 2009; 192:599-603. [PMID: 19915023 DOI: 10.1128/jb.01066-09] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mycobacterium tuberculosis ruvC was induced by DNA damage in a DeltarecA strain despite having an appropriately positioned SOS box to which LexA binds in vitro. An inducible transcript start mapped within the SOS box, and transcriptional fusions identified the promoter. Disruption of the SOS box did not prevent induction, indicating that an alternative mechanism plays a significant role in the control of ruvC expression.
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Khanduja JS, Tripathi P, Muniyappa K. Mycobacterium tuberculosis RuvA induces two distinct types of structural distortions between the homologous and heterologous Holliday junctions. Biochemistry 2009; 48:27-40. [PMID: 19072585 DOI: 10.1021/bi8016526] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A central step in the process of homologous genetic recombination is the strand exchange between two homologous DNA molecules, leading to the formation of the Holliday junction intermediate. Several lines of evidence, both in vitro and in vivo, suggest a concerted role for the Escherichia coli RuvABC protein complex in the process of branch migration and the resolution of the Holliday junctions. A number of investigations have examined the role of RuvA protein in branch migration of the Holliday junction in conjunction with its natural cellular partner, RuvB. However, it remains unclear whether the RuvABC protein complex or its individual subunits function differently in the context of DNA repair and homologous recombination. In this study, we have specifically investigated the function of RuvA protein using Holliday junctions containing either homologous or heterologous arms. Our data show that Mycobacterium tuberculosis ruvA complements E. coli DeltaruvA mutants for survival to genotoxic stress caused by different DNA-damaging agents, and the purified RuvA protein binds HJ in preference to any other substrates. Strikingly, our analysis revealed two distinct types of structural distortions caused by M. tuberculosis RuvA between the homologous and heterologous Holliday junctions. We interpret these data as evidence that local distortion of base pairing in the arms of homologous Holliday junctions by RuvA might augment branch migration catalyzed by RuvB. The biological significance of two modes of structural distortion caused by M. tuberculosis RuvA and the implications for its role in DNA repair and homologous recombination are discussed.
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15
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Abstract
Rad54, a key protein of homologous recombination, physically interacts with a DNA structure-specific endonuclease, Mus81-Eme1. Genetic data indicate that Mus81-Eme1 and Rad54 might function together in the repair of damaged DNA. In vitro, Rad54 promotes branch migration of Holliday junctions, whereas the Mus81-Eme1 complex resolves DNA junctions by endonucleolytic cleavage. Here, we show that human Rad54 stimulates Mus81-Eme1 endonuclease activity on various Holliday junction-like intermediates. This stimulation is the product of specific interactions between the human Rad54 (hRad54) and Mus81 proteins, considering that Saccharomyces cerevisiae Rad54 protein does not stimulate human Mus81-Eme1 endonuclease activity. Stimulation of Mus81-Eme1 cleavage activity depends on formation of specific Rad54 complexes on DNA substrates occurring in the presence of ATP and, to a smaller extent, of other nucleotide cofactors. Thus, our results demonstrate a functional link between the branch migration activity of hRad54 and the structure-specific endonuclease activity of hMus81-Eme1, suggesting that the Rad54 and Mus81-Eme1 proteins may cooperate in the processing of Holliday junction-like intermediates during homologous recombination or DNA repair.
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16
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Hjm/Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro. J Bacteriol 2008; 190:3006-17. [PMID: 18296528 DOI: 10.1128/jb.01662-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Hjm and Hel308a are novel, RecQ-like DNA helicases recently identified in the euryarchaeotes Pyrococcus furiosus and Methanothermobacter thermautotrophicus, respectively. In this study, an Hjm/Hel308 homologue (designated StoHjm) from Sulfolobus tokodaii, a hyperthermophilic archaeon belonging to the Crenarchaeota subdomain of archaea, was cloned, purified, and characterized. Unlike Hjm and Hel308a, which unwind DNA in a 3'-to-5' direction, StoHjm unwound DNA in both 3'-to-5' and 5'-to-3' directions. Remarkably, StoHjm exhibited structure-specific single-stranded-DNA-annealing and fork regression activities in vitro. In addition, gel filtration, affinity pulldown, and yeast two-hybrid analyses revealed that StoHjm physically interacted with StoHjc, the Holliday junction-specific endonuclease from S. tokodaii. This interaction may have functional significance, because the unwinding activity of StoHjm was inhibited by StoHjc in vitro. These results may suggest that the Hjm/Hel308 family helicases, in association with Hjc endonucleases, are involved in processing of stalled replication forks.
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17
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Angeleska A, Jonoska N, Saito M, Landweber LF. RNA-guided DNA assembly. J Theor Biol 2007; 248:706-20. [PMID: 17669433 DOI: 10.1016/j.jtbi.2007.06.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 05/31/2007] [Accepted: 06/06/2007] [Indexed: 10/23/2022]
Abstract
We propose molecular models for homologous DNA recombination events that are guided by either double-stranded RNA (dsRNA) or single-stranded RNA (ssRNA) templates. The models are applied to explain DNA rearrangements in some groups of ciliates, such as Stylonychia or Oxytricha, where extensive gene rearrangement occurs during differentiation of a somatic macronucleus from a germline micronucleus. We describe a model for RNA template guided DNA recombination, such that the template serves as a catalyst that remains unchanged after DNA recombination. This recombination can be seen as topological braiding of the DNA, with the template-guided alignment proceeding through DNA branch migration. We show that a virtual knot diagram can provide a physical representation of the DNA at the time of recombination. Schematically, the braiding process can be represented as a crossing in the virtual knot diagram. The homologous recombination corresponds to removal of the crossings in the knot diagram (called smoothing). We show that if all recombinations are performed at the same time (i.e., simultaneous smoothings of the crossings) then one of the resulting DNA molecules will always contain all of the gene segments in their correct, linear order, which produces the mature DNA sequence.
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Affiliation(s)
- Angela Angeleska
- Department of Mathematics and Statistics, University of South Florida, USA.
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18
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Malo J, Mitchell JC, Vénien-Bryan C, Harris JR, Wille H, Sherratt DJ, Turberfield AJ. Engineering a 2D protein-DNA crystal. Angew Chem Int Ed Engl 2006; 44:3057-61. [PMID: 15828044 DOI: 10.1002/anie.200463027] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jonathan Malo
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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19
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Sanchez H, Kidane D, Reed P, Curtis FA, Cozar MC, Graumann PL, Sharples GJ, Alonso JC. The RuvAB branch migration translocase and RecU Holliday junction resolvase are required for double-stranded DNA break repair in Bacillus subtilis. Genetics 2005; 171:873-83. [PMID: 16020779 PMCID: PMC1456856 DOI: 10.1534/genetics.105.045906] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In models of Escherichia coli recombination and DNA repair, the RuvABC complex directs the branch migration and resolution of Holliday junction DNA. To probe the validity of the E. coli paradigm, we examined the impact of mutations in DeltaruvAB and DeltarecU (a ruvC functional analog) on DNA repair. Under standard transformation conditions we failed to construct DeltaruvAB DeltarecG, DeltarecU DeltaruvAB, DeltarecU DeltarecG, or DeltarecU DeltarecJ strains. However, DeltaruvAB could be combined with addAB (recBCD), recF, recH, DeltarecS, DeltarecQ, and DeltarecJ mutations. The DeltaruvAB and DeltarecU mutations rendered cells extremely sensitive to DNA-damaging agents, although less sensitive than a DeltarecA strain. When damaged cells were analyzed, we found that RecU was recruited to defined double-stranded DNA breaks (DSBs) and colocalized with RecN. RecU localized to these centers at a later time point during DSB repair, and formation was dependent on RuvAB. In addition, expression of RecU in an E. coli ruvC mutant restored full resistance to UV light only when the ruvAB genes were present. The results demonstrate that, as with E. coli RuvABC, RuvAB targets RecU to recombination intermediates and that all three proteins are required for repair of DSBs arising from lesions in chromosomal DNA.
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Affiliation(s)
- Humberto Sanchez
- Centre for Infectious Diseases, Wolfson Research Institute, University of Durham, Stockton-on-Tees TS17 6BH, United Kingdom
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20
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Malo J, Mitchell JC, Vénien-Bryan C, Harris JR, Wille H, Sherratt DJ, Turberfield AJ. Engineering a 2D Protein-DNA Crystal. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200463027] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Ozgenc AI, Szekeres ES, Lawrence CW. In vivo evidence for a recA-independent recombination process in Escherichia coli that permits completion of replication of DNA containing UV damage in both strands. J Bacteriol 2005; 187:1974-84. [PMID: 15743945 PMCID: PMC1064058 DOI: 10.1128/jb.187.6.1974-1984.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have investigated recombination mechanisms promoting the completion of replication in the face of unrepaired DNA damage by transforming an isogenic set of uvrA6 excision-defective Escherichia coli strains with pUC-based plasmids in which each strand carried, at staggered positions, a single thymine-thymine pyrimidine (6-4) pyrimidinone lesion. The distance between the lesions was 28 or 8 bp in one orientation relative to the unidirectional ColE1 origin of replication or, in the other orientation, 30 or 10 bp. C-C mismatches placed opposite each of the T-T photoproducts permit unambiguous detection of the three events that can lead to the completion of replication: sister-strand recombination, translesion replication (TR) on the leading strand, and TR on the lagging strand. We find that E. coli possesses a largely constitutive, recA-independent sister-strand recombination mechanism that allows 9% or more of these severely compromised plasmids to be fully replicated. In one orientation, such recombination depends partly on recG and priA but not on ruvA, ruvB, ruvC, or mutS and is largely independent of recF. In the other orientation, recombination is dependent on none of the genes. The strains used did not contain the cryptic phage encoding recET, which encodes enzymes that promote interplasmid recombination. The nature of the recA-independent recombination mechanism is not known but could perhaps result from a template-strand-switching, or copy choice, process.
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Affiliation(s)
- Ali I Ozgenc
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
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22
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Fujikane R, Komori K, Shinagawa H, Ishino Y. Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus. J Biol Chem 2005; 280:12351-8. [PMID: 15677450 DOI: 10.1074/jbc.m413417200] [Citation(s) in RCA: 43] [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
To identify the branch migration activity in archaea, we fractionated Pyrococcus furiosus cell extracts by several chromatography and assayed for ATP-dependent resolution of synthetic Holliday junctions. The target activity was identified in the column fractions, and the optimal reaction conditions for the branch migration activity were determined using the partially purified fraction. We successfully cloned the corresponding gene by screening a heat-stable protein library made by P. furiosus genomic DNA. The gene, hjm (Holliday junction migration), encodes a protein composed of 720 amino acids. The Hjm protein is conserved in Archaea and belongs to the helicase superfamily 2. A homology search revealed that Hjm shares sequence similarity with the human PolTheta, HEL308, and Drosophila Mus308 proteins, which are involved in a DNA repair, whereas no similar sequences were found in bacteria and yeast. The Hjm helicase may play a central role in the repair systems of organisms living in extreme environments.
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Affiliation(s)
- Ryosuke Fujikane
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan
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23
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Privezentzev CV, Keeley A, Sigala B, Tsaneva IR. The role of RuvA octamerization for RuvAB function in vitro and in vivo. J Biol Chem 2004; 280:3365-75. [PMID: 15556943 DOI: 10.1074/jbc.m409256200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
RuvA plays an essential role in branch migration of the Holliday junction by RuvAB as part of the RuvABC pathway for processing Holliday junctions in Escherichia coli. Two types of RuvA-Holliday junction complexes have been characterized: 1) complex I containing a single RuvA tetramer and 2) complex II in which the junction is sandwiched between two RuvA tetramers. The functional differences between the two forms are still not clear. To investigate the role of RuvA octamerization, we introduced three amino acid substitutions designed to disrupt the E. coli RuvA tetramer-tetramer interface as identified by structural studies. The mutant RuvA was tetrameric and interacted with both RuvB and junction DNA but, as predicted, formed complex I only at protein concentrations up to 500 nm. We present biochemical and surface plasmon resonance evidence for functional and physical interactions of the mutant RuvA with RuvB and RuvC on synthetic junctions. The mutant RuvA with RuvB showed DNA helicase activity and could support branch migration of synthetic four-way and three-way junctions. However, junction binding and the efficiency of branch migration of four-way junctions were affected. The activity of the RuvA mutant was consistent with a RuvAB complex driven by one RuvB hexamer only and lead us to propose that one RuvA tetramer can only support the activity of one RuvB hexamer. Significantly, the mutant failed to complement the UV sensitivity of E. coli DeltaruvA cells. These results indicate strongly that RuvA octamerization is essential for the full biological activity of RuvABC.
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Affiliation(s)
- Cyril V Privezentzev
- Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
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24
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Abstract
Double-strand breaks pose a major threat to the genome and must be repaired accurately if structural and functional integrity are to be preserved. This is usually achieved via homologous recombination, which enables the ends of a broken DNA molecule to engage an intact duplex and prime synthesis of the DNA needed for repair. In Escherichia coli, repair relies on the RecBCD and RecA proteins, the combined ability of which to initiate recombination and form joint-molecule intermediates is well understood. To shed light on subsequent events, we exploited the I-SceI homing endonuclease of yeast to make breaks at I-SceI cleavage sites engineered into the chromosome. We show that survival depends on RecA and RecBCD, and that subsequent events can proceed via either of two pathways, one dependent on the RuvABC Holliday junction resolvase and the other on RecG helicase. Both pathways rely on PriA, presumably to facilitate DNA replication. We discuss the possibility that classical Holliday junctions may not be essential intermediates in repair and consider alternative pathways for RecG-dependent separation of joint molecules formed by RecA.
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Affiliation(s)
- Tom R Meddows
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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25
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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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26
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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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27
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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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28
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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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29
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Prabhu VP, Simons AM, Iwasaki H, Gai D, Simmons DT, Chen J. p53 blocks RuvAB promoted branch migration and modulates resolution of Holliday junctions by RuvC. J Mol Biol 2002; 316:1023-32. [PMID: 11884140 DOI: 10.1006/jmbi.2001.5408] [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: 01/08/2023]
Abstract
The Holliday junction is the central intermediate in homologous recombination. Branch migration of this four-stranded DNA structure is a key step in genetic recombination that affects the extent of genetic information exchanged between two parental DNA molecules. Here, we have constructed synthetic Holliday junctions to test the effects of p53 on both spontaneous and RuvAB promoted branch migration as well as the effect on resolution of the junction by RuvC. We demonstrate that p53 blocks branch migration, and that cleavage of the Holliday junction by RuvC is modulated by p53. These findings suggest that p53 can block branch migration promoted by proteins such as RuvAB and modulate the cleavage by Holliday junction resolution proteins such as RuvC. These results suggest that p53 could have similar effects on eukaryotic homologues of RuvABC and thus have a direct role in recombinational DNA repair.
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Affiliation(s)
- Vidya P Prabhu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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30
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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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31
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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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32
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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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33
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Abstract
The replicative apparatus often encounters blocks to its progression that necessitate removal of the block and reloading of the replication machinery. In Escherichia coli, a major pathway of replication restart involves unwinding of the stalled fork to generate a four-stranded Holliday junction, which can then be cleaved by the RuvABC helicase-endonuclease. This fork regression may be catalyzed by RecG but is thought to occur even in its absence. Here we test whether RuvAB helicase can also catalyze the unwinding of forked DNA to form Holliday junctions. We find that fork DNA is unwound in the direction required for Holliday junction formation only if the loading of RuvB is restricted to the parental duplex DNA arm. If the binding of RuvB is unrestricted, then RuvAB preferentially unwinds forks in the opposite direction. This is probably related to the greater efficiency of two opposed RuvB hexamers operating across a junction compared with a single hexamer. These data argue against RuvAB acting directly at damaged replication forks and imply that other mechanisms must operate in vivo to catalyze Holliday junction formation.
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Affiliation(s)
- P McGlynn
- Institute of Genetics, University of Nottingham, Queen's Medical Center, Nottingham, NG7 2UH, United Kingdom
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34
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Constantinou A, Davies AA, West SC. Branch migration and Holliday junction resolution catalyzed by activities from mammalian cells. Cell 2001; 104:259-68. [PMID: 11207366 DOI: 10.1016/s0092-8674(01)00210-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During homologous recombination, DNA strand exchange leads to Holliday junction formation. The movement, or branch migration, of this junction along DNA extends the length of the heteroduplex joint. In prokaryotes, branch migration and Holliday junction resolution are catalyzed by the RuvA and RuvB proteins, which form a complex with RuvC resolvase to form a "resolvasome". Mammalian cell-free extracts have now been fractionated to reveal analogous activities. An ATP-dependent branch migration activity, which migrates junctions through >2700 bp, cofractionates with the Holliday junction resolvase during several chromatographic steps. Together, the two activities promote concerted branch migration/resolution reactions similar to those catalyzed by E. coli RuvABC, highlighting the preservation of this essential pathway in recombination and DNA repair from prokaryotes to mammals.
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Affiliation(s)
- A Constantinou
- Imperial Cancer Research Fund, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD, Hertfordshire, United Kingdom
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35
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Fogg JM, Lilley DM. Ensuring productive resolution by the junction-resolving enzyme RuvC: large enhancement of the second-strand cleavage rate. Biochemistry 2000; 39:16125-34. [PMID: 11123941 DOI: 10.1021/bi001886m] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RuvC is the principal junction-resolving enzyme of Escherichia coli, cleaving four-way DNA junctions created in homologous recombination. It binds with structural specificity to DNA junctions as a dimer, whereupon each subunit cleaves a phosphodiester bond of diametrically disposed strands. To generate a productive resolution event, these cleavages must be symmetrically located with respect to the point of strand exchange, and in the context of a branch-migrating junction, this requires near-simultaneous cleavage by the two subunits. Using a supercoil-stabilized cruciform as a substrate, we have analyzed the kinetics of strand cleavage. Coordinated bilateral cleavage is not essential in RuvC action, because a heterodimer comprising active and inactive subunits is active in unilateral cleavage. However, in operational terms, fully active RuvC appears to introduce simultaneous cleavages of two strands, because the rate of second-strand cleavage is accelerated by a factor of almost 150 relative to the first. We suggest that relief of strain following the first cleavage could lead to acceleration of subsequent cleavage, and show that DNA junctions rendered more flexible by the presence of strand breaks or bulges are subject to faster cleavage by RuvC. Cleavage of one strand of a junction generated in situ by the action of RuvC can accelerate cleavage at an intrinsically poor site by a factor of 500. Very large rate enhancement of second-strand cleavage by RuvC is likely to be essential to ensure productive resolution of a junction that is being actively branch migrated by the RuvAB machinery.
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Affiliation(s)
- J M Fogg
- CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 4HN, UK
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36
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Gonzalez S, Rosenfeld A, Szeto D, Wetmur JG. The ruv proteins of Thermotoga maritima: branch migration and resolution of Holliday junctions. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1494:217-25. [PMID: 11121578 DOI: 10.1016/s0167-4781(00)00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In homologous recombination in bacteria, the RuvAB Holliday junction-specific helicase catalyzes Holliday junction branch migration, and the RuvC Holliday junction resolvase catalyzes formation of spliced or patched structures. RuvAB and RuvC from the hyperthermophile Thermotoga maritima were expressed in Escherichia coli and purified to homogeneity. An inverted repeat sequence with unique termini was produced by PCR, restriction endonuclease cleavage, and head-to-tail ligation. A second inverted repeat sequence was derived by amplification of a second template containing a three-nucleotide insertion. Reassociation products from a mixture of these two sequences were homoduplex linear molecules and heteroduplex heat-stable Holliday junctions, which acted as substrates for both T. maritima RuvAB and RuvC. The T. maritima RuvAB helicase catalyzed energy-dependent Holliday junction branch migration at 70 degrees C, leading to heteroduplex linear duplex molecules with two three-nucleotide loops. Either ATP or ATP gamma S hydrolysis served as the energy source. T. maritima RuvC resolved Holliday junctions at 70 degrees C. Remarkably, the cleavage site was identical to the preferred cleavage site for E. coli RuvC [(A/T)TT(downward arrow)(G/C)]. The conservation of function and the ease of purification of wild-type and mutant thermophilic proteins argues for the use of T. maritima proteins for additional biochemical and structural studies.
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Affiliation(s)
- S Gonzalez
- Department of Microbiology, Mount Sinai School of Medicine, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA
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37
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Bolt EL, Sharples GJ, Lloyd RG. Analysis of conserved basic residues associated with DNA binding (Arg69) and catalysis (Lys76) by the RusA holliday junction resolvase. J Mol Biol 2000; 304:165-76. [PMID: 11080453 DOI: 10.1006/jmbi.2000.4196] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Holliday junctions are key intermediates in both homologous recombination and DNA repair, and are also formed from replication forks stalled at lesions in the template strands. Their resolution is critical for chromosome segregation and cell viability, and is mediated by a class of small, homodimeric endonucleases that bind the structure and cleave the DNA. All the enzymes studied require divalent metal ions for strand cleavage and their active centres are characterised by conserved aspartate/glutamate residues that provide ligands for metal binding. Sequence alignments reveal that they also contain a number of conserved basic residues. We used site-directed mutagenesis to investigate such residues in the RusA resolvase. RusA is a 120 amino acid residue polypeptide that can be activated in Escherichia coli to promote recombination and repair in the absence of the Ruv proteins. The RuvA, RuvB and RuvC proteins form a complex on Holliday junction DNA that drives coupled branch migration (RuvAB) and resolution (RuvC) reactions. In contrast to RuvC, the RusA resolvase does not interact directly with a branch migration motor, which simplifies analysis of its resolution activity. Catalysis depends on three highly conserved acidic residues (Asp70, Asp72 and Asp91) that define the catalytic centre. We show that Lys76, which is invariant in RusA sequences, is essential for catalysis, but not for DNA binding, and that an invariant asparagine residue (Asn73) is required for optimal activity. Analysis of DNA binding revealed that RusA may interact with one face of an open junction before manipulating its conformation in the presence of Mg(2+) as part of the catalytic process. A well-conserved arginine residue (Arg69) is linked with this critical stage. These findings provide the first insights into the roles played by basic residues in DNA binding and catalysis by a Holliday junction resolvase.
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Affiliation(s)
- E L Bolt
- Institute of Genetics, University of Nottingham, Nottingham, NG7 2UH, UK
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38
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Ingleston SM, Sharples GJ, Lloyd RG. The acidic pin of RuvA modulates Holliday junction binding and processing by the RuvABC resolvasome. EMBO J 2000; 19:6266-74. [PMID: 11080172 PMCID: PMC305816 DOI: 10.1093/emboj/19.22.6266] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Holliday junctions are four-way branched DNA structures formed during recombination, replication and repair. They are processed in Escherichia coli by the RuvA, RuvB and RuvC proteins. RuvA targets the junction and facilitates loading of RuvB helicase and RuvC endonuclease to form complexes that catalyse junction branch migration (RuvAB) and resolution (RuvABC). We investigated the role of RuvA in these reactions and in particular the part played by the acidic pin located on its DNA-binding surface. By making appropriate substitutions of two key amino acids (Glu55 and Asp56), we altered the charge on the pin and investigated how this affected junction binding and processing. We show that two negative charges on each subunit of the pin are crucial. They facilitate junction targeting by preventing binding to duplex DNA and also constrain branch migration by RuvAB in a manner critical for junction processing. These findings provide the first direct evidence that RuvA has a mechanistic role in branch migration. They also provide insight into the coupling of branch migration and resolution by the RuvABC resolvasome.
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Affiliation(s)
- S M Ingleston
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
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39
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Abstract
The Holliday junction is a central intermediate in homologous recombination. It consists of a four-way structure that can be resolved by cleavage to give either the crossover or noncrossover products observed. We show here that the formation of these products is controlled by the E. coli resolvasome (RuvABC) in such way that double-strand break repair (DSBR) leads to crossing over and single-strand gap repair (SSGR) does not lead to crossing over. We argue that the positioning of the RuvABC complex and its consequent direction of junction-cleavage is not random. In fact, the action of the RuvABC complex avoids crossing over in the most commonly predicted situations where Holliday junctions are encountered in DNA replication and repair. Our observations suggest that the positioning of the resolvasome may provide a general biochemical mechanism by which cells can control crossing over in recombination.
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Affiliation(s)
- G A Cromie
- Institute of Cell and Molecular Biology, University of Edinburgh, United Kingdom
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40
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Eggleston AK, West SC. Cleavage of holliday junctions by the Escherichia coli RuvABC complex. J Biol Chem 2000; 275:26467-76. [PMID: 10851230 DOI: 10.1074/jbc.m001496200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli RuvABC proteins process recombination intermediates during genetic recombination and recombinational repair. Although early biochemical studies indicated distinct RuvAB-mediated branch migration and RuvC-mediated Holliday junction resolution reactions, more recent studies have shown that the three proteins act together as a "resolvasome" complex. In this work we have used recombination intermediates made by RecA to determine whether the RuvAB proteins affect the sequence specificity of the RuvC resolvase. We find that RuvAB proteins do not alter significantly the site specificity of RuvC-dependent cleavage, although under certain conditions, they do affect the efficiency of cleavage at particular sites. The presence of RecA also influences cleavage at some sites. We also show that the RuvAB proteins act upon transient strand exchange intermediates made using substrates that have the opposite polarity of those preferred by RecA. Together, our results allow us to develop further a model for the recombinational repair of DNA lesions that lead to the formation of post-replication gaps during DNA replication. The novel features of this model are as follows: (i) the RuvABC resolvasome recognizes joints made by RecA; (ii) resolution by RuvABC occurs at specific sites containing the RuvC consensus cleavage sequence 5'-(A/T)TT downward arrow(G/C)-3'; and (iii) Holliday junction resolution often occurs close to the initiating gap without significant heteroduplex DNA formation.
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Affiliation(s)
- A K Eggleston
- Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, United Kingdom
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41
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Arenas-Licea J, van Gool AJ, Keeley AJ, Davies A, West SC, Tsaneva IR. Functional interactions of Mycobacterium leprae RuvA with Escherichia coli RuvB and RuvC on holliday junctions. J Mol Biol 2000; 301:839-50. [PMID: 10966790 DOI: 10.1006/jmbi.2000.4009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Mycobacterium leprae RuvA homologue (MlRuvA) was over-expressed in Escherichia coli and purified to homogeneity. The DNA-binding specificity and the functional interactions of MlRuvA with E. coli RuvB and RuvC (EcRuvB and EcRuvC) were examined using synthetic Holliday junctions. MlRuvA bound specifically to Holliday junctions and produced similar band-shift patterns as EcRuvA. Moreover, MlRuvA formed functional DNA helicase and branch-migration enzymes with EcRuvB, although the heterologous enzyme had a lower efficiency. These results demonstrate that the RuvA homologue of M. leprae is a functional branch-migration subunit. Whereas MlRuvA promoted branch-migration in combination with EcRuvB, it was unable to stimulate branch-migration-dependent resolution in a RuvABC complex. The inability to stimulate RuvC was not due to its failure to form heterologous RuvABC complexes on junctions, since such complexes were detected by co-immunoprecipitation. Most likely, the stability of the heterologous RuvABC complex and, possibly, the interactions between RuvA and RuvC were impaired, as gel-shift experiments failed to show mixed MlRuvA-EcRuvC-junction complexes. These results demonstrate that branch-migration per se and the assembly of a RuvABC complex on the Holliday junction are insufficient for RuvAB-dependent resolution of the junction by RuvC, suggesting that specific and intimate interactions between all three proteins are required for the function of a RuvABC "resolvasome".
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Affiliation(s)
- J Arenas-Licea
- Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, UK
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42
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Miyata T, Yamada K, Iwasaki H, Shinagawa H, Morikawa K, Mayanagi K. Two different oligomeric states of the RuvB branch migration motor protein as revealed by electron microscopy. J Struct Biol 2000; 131:83-9. [PMID: 11042078 DOI: 10.1006/jsbi.2000.4290] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In prokaryotes, the RuvA, B, and C proteins play major roles at the late stage of DNA homologous recombination, where RuvB complexed with RuvA acts as an ATP-dependent motor for branch migration. The oligomeric structures of negatively stained and frozen hydrated RuvB from Thermus thermophilus HB8 were investigated by electron microscopy. RuvB oligomers free of DNA formed a ring structure of about 14 nm in diameter. The averaged top view image clearly indicated a sevenfold symmetry, suggesting that it exists as a heptamer. The RuvB oligomers complexed with duplex DNA formed a smaller ring of about 13 nm in diameter. The averaged top view images represented a sixfold symmetry. This difference in oligomerization indicates that the oligomeric structure of RuvB may convert from a heptamer to a hexamer upon DNA binding. In addition, this finding provides the lesson that great care should be taken in investigating the subunit organizations of DNA binding proteins, because their oligomeric states are more sensitive to DNA interactions than expected.
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Affiliation(s)
- T Miyata
- Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, 565-0874, Japan
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43
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Ariyoshi M, Nishino T, Iwasaki H, Shinagawa H, Morikawa K. Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer. Proc Natl Acad Sci U S A 2000; 97:8257-62. [PMID: 10890893 PMCID: PMC26934 DOI: 10.1073/pnas.140212997] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2000] [Accepted: 05/11/2000] [Indexed: 11/18/2022] Open
Abstract
In the major pathway of homologous DNA recombination in prokaryotic cells, the Holliday junction intermediate is processed through its association with RuvA, RuvB, and RuvC proteins. Specific binding of the RuvA tetramer to the Holliday junction is required for the RuvB motor protein to be loaded onto the junction DNA, and the RuvAB complex drives the ATP-dependent branch migration. We solved the crystal structure of the Holliday junction bound to a single Escherichia coli RuvA tetramer at 3.1-A resolution. In this complex, one side of DNA is accessible for cleavage by RuvC resolvase at the junction center. The refined junction DNA structure revealed an open concave architecture with a four-fold symmetry. Each arm, with B-form DNA, in the Holliday junction is predominantly recognized in the minor groove through hydrogen bonds with two repeated helix-hairpin-helix motifs of each RuvA subunit. The local conformation near the crossover point, where two base pairs are disrupted, suggests a possible scheme for successive base pair rearrangements, which may account for smooth Holliday junction movement without segmental unwinding.
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Affiliation(s)
- M Ariyoshi
- Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
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44
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Nishino T, Iwasaki H, Kataoka M, Ariyoshi M, Fujita T, Shinagawa H, Morikawa K. Modulation of RuvB function by the mobile domain III of the Holliday junction recognition protein RuvA. J Mol Biol 2000; 298:407-16. [PMID: 10772859 DOI: 10.1006/jmbi.2000.3675] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In prokaryotes, RuvA-RuvB complexes play a crucial role in the migration of the Holliday junction, which is a key intermediate of homologous recombination. RuvA binds to the Holliday junction and enhances the ATPase activity of RuvB required for branch migration. RuvA adopts a unique domain structure, which assembles into a tetrameric molecule. The previous mutational and proteolytic analyses suggested that mutations in a carboxyl-terminal domain (domain III) impair binding of RuvA to RuvB. In order to clarify the functional role of each domain in vitro, we established the recombinant expression systems, which allow us to analyze structural and biochemical properties of each domain separately. A small-angle X-ray scattering solution study, combined with X-ray crystallographic analyses, was applied to the tetrameric full-length RuvA and its tetrameric NH2 region (domains I and II) lacking the domain III. These results demonstrated that domain III can be completely separate from the tetrameric major core of the NH2 region and freely mobile in solution, through a remarkably flexible loop. Biochemical analyses indicated that domain III not only interacts with RuvB, but also modulates its ATPase activity. This modulation may facilitate the dynamic coupling between RuvA and RuvB during branch migration.
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Affiliation(s)
- T Nishino
- Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Osaka, Suita, 565-0874, Japan
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45
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McGlynn P, Lloyd RG. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell 2000; 101:35-45. [PMID: 10778854 DOI: 10.1016/s0092-8674(00)80621-2] [Citation(s) in RCA: 247] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have discovered a correlation between the ability of Escherichia coli cells to survive damage to DNA and their ability to modulate RNA polymerase via the stringent response regulators, (p)ppGpp. Elevation of (p)ppGpp, or certain mutations in the beta subunit of RNA polymerase, dramatically improve survival of UV-irradiated strains lacking the RuvABC Holliday junction resolvase. Increased survival depends on excision and recombination proteins and relies on the ability of RecG helicase to form Holliday junctions from replication forks stalled at lesions in the DNA and of PriA to initiate replication restart. The role of RecG provides novel insights into the interplay between transcription, replication, and recombination, and suggests a general model in which recombination underpins genome duplication in the face of frequent obstacles to replication fork progression.
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Affiliation(s)
- P McGlynn
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, United Kingdom
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46
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Déclais AC, Lilley DM. Extensive central disruption of a four-way junction on binding CCE1 resolving enzyme. J Mol Biol 2000; 296:421-33. [PMID: 10669598 DOI: 10.1006/jmbi.1999.3479] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Junction-resolving enzymes are nucleases that are selective for the structure of the four-way DNA junction that is important in genetic recombination. They exhibit selectivity for the structure of the junction, but they also manipulate the structure. Local disruption of DNA structure around the centre of the junction by CCE1 of Saccharomyces cerevisiae has been investigated using 2-aminopurine fluorescence. On binding CCE1, 2-aminopurine bases located at the point of strand exchange exhibit a large increase in fluorescence intensity (up to 39-fold enhancement), consistent with complete unstacking. This was observed for all positions around the centre of the junction, both 5' and 3' to the point of strand exchange. Thymine bases complementary to the modified adenine bases adjacent to the junction centre were strongly reactive to potassium permanganate. The results indicate that binding of CCE1 results in a complete unpairing of the four central base-pairs of the junction, with a lesser disruption of the next base-pairs.
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Affiliation(s)
- A C Déclais
- Department of Biochemistry, CRC Nucleic Acid Structure Research Group, Dundee, DD1 4HN, UK
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47
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Kuzminov A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol Biol Rev 1999; 63:751-813, table of contents. [PMID: 10585965 PMCID: PMC98976 DOI: 10.1128/mmbr.63.4.751-813.1999] [Citation(s) in RCA: 719] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although homologous recombination and DNA repair phenomena in bacteria were initially extensively studied without regard to any relationship between the two, it is now appreciated that DNA repair and homologous recombination are related through DNA replication. In Escherichia coli, two-strand DNA damage, generated mostly during replication on a template DNA containing one-strand damage, is repaired by recombination with a homologous intact duplex, usually the sister chromosome. The two major types of two-strand DNA lesions are channeled into two distinct pathways of recombinational repair: daughter-strand gaps are closed by the RecF pathway, while disintegrated replication forks are reestablished by the RecBCD pathway. The phage lambda recombination system is simpler in that its major reaction is to link two double-stranded DNA ends by using overlapping homologous sequences. The remarkable progress in understanding the mechanisms of recombinational repair in E. coli over the last decade is due to the in vitro characterization of the activities of individual recombination proteins. Putting our knowledge about recombinational repair in the broader context of DNA replication will guide future experimentation.
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Affiliation(s)
- A Kuzminov
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA.
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48
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George H, Mézard C, Stasiak A, West SC. Helicase-defective RuvB(D113E) promotes RuvAB-mediated branch migration in vitro. J Mol Biol 1999; 293:505-19. [PMID: 10543946 DOI: 10.1006/jmbi.1999.3187] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Escherichia coli, the RuvA and RuvB proteins interact at Holliday junctions to promote branch migration leading to the formation of heteroduplex DNA. RuvA provides junction-binding specificity and RuvB drives ATP-dependent branch migration. Since RuvB contains sequence motifs characteristic of a DNA helicase and RuvAB exhibit helicase activity in vitro, we have analysed the role of DNA unwinding in relation to branch migration. A mutant RuvB protein, RuvB(D113E), mutated in helicase motif II (the DExx box), has been purified to homogeneity. The mutant protein forms hexameric rings on DNA similar to those formed by wild-type protein and promotes branch migration in the presence of RuvA. However, RuvB(D113E) exhibits reduced ATPase activity and is severely compromised in its DNA helicase activity. Models for RuvAB-mediated branch migration that invoke only limited DNA unwinding activity are proposed.
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MESH Headings
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/isolation & purification
- Adenosine Triphosphatases/metabolism
- Adenosine Triphosphate/metabolism
- Amino Acid Motifs
- Amino Acid Sequence
- Amino Acid Substitution
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/isolation & purification
- Bacterial Proteins/metabolism
- DNA/chemistry
- DNA/genetics
- DNA/metabolism
- DNA/ultrastructure
- DNA Helicases/chemistry
- DNA Helicases/genetics
- DNA Helicases/isolation & purification
- DNA Helicases/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA-Binding Proteins/metabolism
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Escherichia coli Proteins
- Genes, Bacterial/genetics
- Genes, Bacterial/physiology
- Kinetics
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Nucleic Acid Heteroduplexes/chemistry
- Nucleic Acid Heteroduplexes/genetics
- Nucleic Acid Heteroduplexes/metabolism
- Phenotype
- Recombination, Genetic/genetics
- Ultraviolet Rays
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Affiliation(s)
- H George
- Clare Hall Laboratories, Imperial Cancer Research Fund, South Mimms, Herts, EN6 3LD, UK
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49
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Cox MM. Recombinational DNA repair in bacteria and the RecA protein. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 63:311-66. [PMID: 10506835 DOI: 10.1016/s0079-6603(08)60726-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In bacteria, the major function of homologous genetic recombination is recombinational DNA repair. This is not a process reserved only for rare double-strand breaks caused by ionizing radiation, nor is it limited to situations in which the SOS response has been induced. Recombinational DNA repair in bacteria is closely tied to the cellular replication systems, and it functions to repair damage at stalled replication forks, Studies with a variety of rec mutants, carried out under normal aerobic growth conditions, consistently suggest that at least 10-30% of all replication forks originating at the bacterial origin of replication are halted by DNA damage and must undergo recombinational DNA repair. The actual frequency may be much higher. Recombinational DNA repair is both the most complex and the least understood of bacterial DNA repair processes. When replication forks encounter a DNA lesion or strand break, repair is mediated by an adaptable set of pathways encompassing most of the enzymes involved in DNA metabolism. There are five separate enzymatic processes involved in these repair events: (1) The replication fork assembled at OriC stalls and/or collapses when encountering DNA damage. (2) Recombination enzymes provide a complementary strand for a lesion isolated in a single-strand gap, or reconstruct a branched DNA at the site of a double-strand break. (3) The phi X174-type primosome (or repair primosome) functions in the origin-independent reassembly of the replication fork. (4) The XerCD site-specific recombination system resolves the dimeric chromosomes that are the inevitable by-product of frequent recombination associated with recombinational DNA repair. (5) DNA excision repair and other repair systems eliminate lesions left behind in double-stranded DNA. The RecA protein plays a central role in the recombination phase of the process. Among its many activities, RecA protein is a motor protein, coupling the hydrolysis of ATP to the movement of DNA branches.
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Affiliation(s)
- M M Cox
- Department of Biochemistry, University of Wisconsin-Madison 53706, USA
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50
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Sharples GJ, Ingleston SM, Lloyd RG. Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J Bacteriol 1999; 181:5543-50. [PMID: 10482492 PMCID: PMC94071 DOI: 10.1128/jb.181.18.5543-5550.1999] [Citation(s) in RCA: 143] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- G J Sharples
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom.
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