1
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Balakrishnan S, Adolph M, Tsai MS, Akizuki T, Gallagher K, Cortez D, Chazin WJ. Structure of RADX and mechanism for regulation of RAD51 nucleofilaments. Proc Natl Acad Sci U S A 2024; 121:e2316491121. [PMID: 38466836 PMCID: PMC10962997 DOI: 10.1073/pnas.2316491121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Replication fork reversal is a fundamental process required for resolution of encounters with DNA damage. A key step in the stabilization and eventual resolution of reversed forks is formation of RAD51 nucleoprotein filaments on exposed single strand DNA (ssDNA). To avoid genome instability, RAD51 filaments are tightly controlled by a variety of positive and negative regulators. RADX (RPA-related RAD51-antagonist on the X chromosome) is a recently discovered negative regulator that binds tightly to ssDNA, directly interacts with RAD51, and regulates replication fork reversal and stabilization in a context-dependent manner. Here, we present a structure-based investigation of RADX's mechanism of action. Mass photometry experiments showed that RADX forms multiple oligomeric states in a concentration-dependent manner, with a predominance of trimers in the presence of ssDNA. The structure of RADX, which has no structurally characterized orthologs, was determined ab initio by cryo-electron microscopy (cryo-EM) from maps in the 2 to 4 Å range. The structure reveals the molecular basis for RADX oligomerization and the coupled multi-valent binding of ssDNA binding. The interaction of RADX with RAD51 filaments was imaged by negative stain EM, which showed a RADX oligomer at the end of filaments. Based on these results, we propose a model in which RADX functions by capping and restricting the end of RAD51 filaments.
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Affiliation(s)
- Swati Balakrishnan
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Madison Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Miaw-Sheue Tsai
- Biological Systems and Bioengineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Tae Akizuki
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Kaitlyn Gallagher
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Walter J. Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
- Department of Chemistry, Vanderbilt University, Nashville, TN37235
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2
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ATPase Activity of Bacillus subtilis RecA Affects the Dynamic Formation of RecA Filaments at DNA Double Strand Breaks. mSphere 2022; 7:e0041222. [PMID: 36321831 PMCID: PMC9769622 DOI: 10.1128/msphere.00412-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
RecA plays a central role in DNA repair and is a main actor involved in homologous recombination (HR). In vivo, RecA forms filamentous structures termed "threads," which are essential for HR, but whose nature is still ill defined. We show that RecA from Bacillus subtilis having lower ATP binding activity can still form nucleoprotein filaments in vitro, features lower dsDNA binding activity, but still retains most of wild type RecA activity in vivo. Contrarily, loss of ATPase activity strongly reduced formation of nucleoprotein filaments in vitro, and effectivity to repair double strand breaks (DSBs) in vivo. In the presence of wild type RecA protein, additionally expressed RecA with lowered ATPbinding activity only moderately affected RecA dynamics, while loss of ATPase activity leads to a large reduction of the formation of threads, as well as of their dynamic changes observed in a seconds-scale. Single molecule tracking of RecA revealed incorporation of freely diffusing and nonspecifically DNA-bound molecules into threads upon induction of a single DSB. This change of dynamics was highly perturbed in the absence of ATPase activity, revealing that filamentous forms of RecA as well as their dynamics depend on ATPase activity. Based on the idea that ATPase activity of RecA is most important for DNA strand exchange activity, our data suggest that extension and retraction of threads due is to many local strand invasion events during the search for sequences homologous to the induced DNA break site. IMPORTANCE Single-strand (ss) DNA binding ATPase RecA is the central recombinase in homologous recombination, and therefore essential for DNA repair pathways involving DNA strand exchange reactions. In several bacterial, RecA forms filamentous structures along the long axis of cells after induction of double strand breaks (DSBs) in the chromosome. These striking assemblies likely reflect RecA/ssDNA nucleoprotein filaments, which can extend and remodel within a time frame of few minutes. We show that ATPase activity of RecA is pivotal for these dynamic rearrangements, which include recruitment of freely diffusing molecules into low-mobile molecules within filaments. Our data suggest that ssDNA binding- and unbinding reactions are at the heart of RecA dynamics that power the dynamics of subcellular filamentous assemblies, leading to strand exchange reactions over a distance of several micrometers.
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3
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Purkait D, Islam F, Mishra PP. A single-molecule approach to unravel the molecular mechanism of the action of Deinococcus radiodurans RecD2 and its interaction with SSB and RecA in DNA repair. Int J Biol Macromol 2022; 221:653-664. [PMID: 36096248 DOI: 10.1016/j.ijbiomac.2022.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022]
Abstract
Helicases are ATP-driven molecular machines that directionally remodel nucleic acid polymers in all three domains of life. They are responsible for resolving double-stranded DNA (dsDNA) into single-strands, which is essential for DNA replication, nucleotide excision repair, and homologous recombination. RecD2 from Deinococcus radiodurans (DrRecD2) has important contributions to the organism's unusually high tolerance to gamma radiation and hydrogen peroxide. Although the results from X-ray Crystallography studies have revealed the structural characteristics of the protein, direct experimental evidence regarding the dynamics of the DNA unwinding process by DrRecD2 in the context of other accessory proteins is yet to be found. In this study, we have probed the exact binding event and processivity of DrRecD2 at single-molecule resolution using Protein-induced fluorescence enhancement (smPIFE) and Forster resonance energy transfer (smFRET). We have found that the protein prefers to bind at the 5' terminal end of the single-stranded DNA (ssDNA) by Drift and has helicase activity even in absence of ATP. However, a faster and iterative mode of DNA unwinding was evident in presence of ATP. The rate of translocation of the protein was found to be slower on dsDNA compared to ssDNA. We also showed that DrRecD2 is recruited at the binding site by the single-strand binding protein (SSB) and during the unwinding, it can displace RecA from ssDNA.
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Affiliation(s)
- Debayan Purkait
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India
| | - Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India
| | - Padmaja P 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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Bianco PR, Lu Y. Single-molecule insight into stalled replication fork rescue in Escherichia coli. Nucleic Acids Res 2021; 49:4220-4238. [PMID: 33744948 PMCID: PMC8096234 DOI: 10.1093/nar/gkab142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 01/05/2023] Open
Abstract
DNA replication forks stall at least once per cell cycle in Escherichia coli. DNA replication must be restarted if the cell is to survive. Restart is a multi-step process requiring the sequential action of several proteins whose actions are dictated by the nature of the impediment to fork progression. When fork progress is impeded, the sequential actions of SSB, RecG and the RuvABC complex are required for rescue. In contrast, when a template discontinuity results in the forked DNA breaking apart, the actions of the RecBCD pathway enzymes are required to resurrect the fork so that replication can resume. In this review, we focus primarily on the significant insight gained from single-molecule studies of individual proteins, protein complexes, and also, partially reconstituted regression and RecBCD pathways. This insight is related to the bulk-phase biochemical data to provide a comprehensive review of each protein or protein complex as it relates to stalled DNA replication fork rescue.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yue Lu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
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5
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Maman N, Kumar P, Yadav A, Feingold M. Single Molecule Study of the Polymerization of RecA on dsDNA: The Dynamics of Individual Domains. Front Mol Biosci 2021; 8:609076. [PMID: 33842536 PMCID: PMC8025788 DOI: 10.3389/fmolb.2021.609076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
In the Escherichia coli, RecA plays a central role in the recombination and repair of the DNA. For homologous recombination, RecA binds to ssDNA forming a nucleoprotein filament. The RecA-ssDNA filament searches for a homologous sequence on a dsDNA and, subsequently, RecA mediates strand exchange between the ssDNA and the dsDNA. In vitro, RecA binds to both ssDNA and dsDNA. Despite a wide range of studies of the polymerization of RecA on dsDNA, both at the single molecule level and by means of biochemical methods, important aspects of this process are still awaiting a better understanding. Specifically, a detailed, quantitative description of the nucleation and growth dynamics of the RecA-dsDNA filaments is still lacking. Here, we use Optical Tweezers together with a single molecule analysis approach to measure the dynamics of the individual RecA domains on dsDNA and the corresponding growth rates for each of their fronts. We focus on the regime where the nucleation and growth rate constants, kn and kg, are comparable, leading to a coverage of the dsDNA molecule that consists of a small number of RecA domains. For the case of essentially irreversible binding (using ATPγS instead of ATP), we find that domain growth is highly asymmetric with a ratio of about 10:1 between the fast and slow fronts growth rates.
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Affiliation(s)
- Nitzan Maman
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,The Ilse Katz Center for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Pramod Kumar
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Amarjeet Yadav
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Mario Feingold
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,The Ilse Katz Center for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva, Israel
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6
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Nevinsky GA. How Enzymes, Proteins, and Antibodies Recognize Extended DNAs; General Regularities. Int J Mol Sci 2021; 22:1369. [PMID: 33573045 PMCID: PMC7866405 DOI: 10.3390/ijms22031369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/17/2022] Open
Abstract
X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and proteins with long DNA and RNA at the quantitative molecular level can be successfully analyzed using the method of the stepwise increase in ligand complexity (SILC). The present review summarizes the data on stepwise increase in ligand complexity (SILC) analysis of nucleic acid recognition by various enzymes-replication, restriction, integration, topoisomerization, six different repair enzymes (uracil DNA glycosylase, Fpg protein from Escherichia coli, human 8-oxoguanine-DNA glycosylase, human apurinic/apyrimidinic endonuclease, RecA protein, and DNA-ligase), and five DNA-recognizing proteins (RNA helicase, human lactoferrin, alfa-lactalbumin, human blood albumin, and IgGs against DNA). The relative contributions of structural elements of DNA fragments "covered" by globules of enzymes and proteins to the total affinity of DNA have been evaluated. Thermodynamic and catalytic factors providing discrimination of unspecific and specific DNAs by these enzymes on the stages of primary complex formation following changes in enzymes and DNAs or RNAs conformations and direct processing of the catalysis of the reactions were found. General regularities of recognition of nucleic acid by DNA-dependent enzymes, proteins, and antibodies were established.
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Affiliation(s)
- Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 63009 Novosibirsk, Russia
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7
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A Comprehensive View of Translesion Synthesis in Escherichia coli. Microbiol Mol Biol Rev 2020; 84:84/3/e00002-20. [PMID: 32554755 DOI: 10.1128/mmbr.00002-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The lesion bypass pathway, translesion synthesis (TLS), exists in essentially all organisms and is considered a pathway for postreplicative gap repair and, at the same time, for lesion tolerance. As with the saying "a trip is not over until you get back home," studying TLS only at the site of the lesion is not enough to understand the whole process of TLS. Recently, a genetic study uncovered that polymerase V (Pol V), a poorly expressed Escherichia coli TLS polymerase, is not only involved in the TLS step per se but also participates in the gap-filling reaction over several hundred nucleotides. The same study revealed that in contrast, Pol IV, another highly expressed TLS polymerase, essentially stays away from the gap-filling reaction. These observations imply fundamentally different ways these polymerases are recruited to DNA in cells. While access of Pol IV appears to be governed by mass action, efficient recruitment of Pol V involves a chaperone-like action of the RecA filament. We present a model of Pol V activation: the 3' tip of the RecA filament initially stabilizes Pol V to allow stable complex formation with a sliding β-clamp, followed by the capture of the terminal RecA monomer by Pol V, thus forming a functional Pol V complex. This activation process likely determines higher accessibility of Pol V than of Pol IV to normal DNA. Finally, we discuss the biological significance of TLS polymerases during gap-filling reactions: error-prone gap-filling synthesis may contribute as a driving force for genetic diversity, adaptive mutation, and evolution.
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8
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Lin YH, Chu CC, Fan HF, Wang PY, Cox MM, Li HW. A 5'-to-3' strand exchange polarity is intrinsic to RecA nucleoprotein filaments in the absence of ATP hydrolysis. Nucleic Acids Res 2019; 47:5126-5140. [PMID: 30916331 PMCID: PMC6547424 DOI: 10.1093/nar/gkz189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
RecA is essential to recombinational DNA repair in which RecA filaments mediate the homologous DNA pairing and strand exchange. Both RecA filament assembly and the subsequent DNA strand exchange are directional. Here, we demonstrate that the polarity of DNA strand exchange is embedded within RecA filaments even in the absence of ATP hydrolysis, at least over short DNA segments. Using single-molecule tethered particle motion, we show that successful strand exchange in the presence of ATP proceeds with a 5′-to-3′ polarity, as demonstrated previously. RecA filaments prepared with ATPγS also exhibit a 5′-to-3′ progress of strand exchange, suggesting that the polarity is not determined by RecA disassembly and/or ATP hydrolysis. RecAΔC17 mutants, lacking a C-terminal autoregulatory flap, also promote strand exchange in a 5′-to-3′ polarity in ATPγS, a polarity that is largely lost with this RecA variant when ATP is hydrolyzed. We propose that there is an inherent strand exchange polarity mediated by the structure of the RecA filament groove, associated by conformation changes propagated in a polar manner as DNA is progressively exchanged. ATP hydrolysis is coupled to polar strand exchange over longer distances, and its contribution to the polarity requires an intact RecA C-terminus.
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Affiliation(s)
- Yu-Hsuan Lin
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Chia-Chieh Chu
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 11221 Taiwan
| | - Pang-Yen Wang
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin, Madison, 53706, USA
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, 10617, Taiwan
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9
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Keyamura K, Hishida T. Topological DNA-binding of structural maintenance of chromosomes-like RecN promotes DNA double-strand break repair in Escherichia coli. Commun Biol 2019; 2:413. [PMID: 31754643 PMCID: PMC6856136 DOI: 10.1038/s42003-019-0655-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial RecN, closely related to the structural maintenance of chromosomes (SMC) family of proteins, functions in the repair of DNA double-strand breaks (DSBs) by homologous recombination. Here we show that the purified Escherichia coli RecN protein topologically loads onto both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) that has a preference for ssDNA. RecN topologically bound to dsDNA slides off the end of linear dsDNA, but this is prevented by RecA nucleoprotein filaments on ssDNA, thereby allowing RecN to translocate to DSBs. Furthermore, we found that, once RecN is recruited onto ssDNA, it can topologically capture a second dsDNA substrate in an ATP-dependent manner, suggesting a role in synapsis. Indeed, RecN stimulates RecA-mediated D-loop formation and subsequent strand exchange activities. Our findings provide mechanistic insights into the recruitment of RecN to DSBs and sister chromatid interactions by RecN, both of which function in RecA-mediated DSB repair.
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Affiliation(s)
- Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
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10
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Tashjian TF, Danilowicz C, Molza AE, Nguyen BH, Prévost C, Prentiss M, Godoy VG. Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair. J Biol Chem 2019; 294:7588-7600. [PMID: 30872406 DOI: 10.1074/jbc.ra118.006233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/28/2019] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily conserved Escherichia coli translesion DNA polymerase IV (DinB) is one of three enzymes that can bypass potentially deadly DNA lesions on the template strand during DNA replication. Remarkably, however, DinB is the only known translesion DNA polymerase active in RecA-mediated strand exchange during error-prone double-strand break repair. In this process, a single-stranded DNA (ssDNA)-RecA nucleoprotein filament invades homologous dsDNA, pairing the ssDNA with the complementary strand in the dsDNA. When exchange reaches the 3' end of the ssDNA, a DNA polymerase can add nucleotides onto the end, using one strand of dsDNA as a template and displacing the other. It is unknown what makes DinB uniquely capable of participating in this reaction. To explore this topic, we performed molecular modeling of DinB's interactions with the RecA filament during strand exchange, identifying key contacts made with residues in the DinB fingers domain. These residues are highly conserved in DinB, but not in other translesion DNA polymerases. Using a novel FRET-based assay, we found that DinB variants with mutations in these conserved residues are less effective at stabilizing RecA-mediated strand exchange than native DinB. Furthermore, these variants are specifically deficient in strand displacement in the absence of RecA filament. We propose that the amino acid patch of highly conserved residues in DinB-like proteins provides a mechanistic explanation for DinB's function in strand exchange and improves our understanding of recombination by providing evidence that RecA plays a role in facilitating DinB's activity during strand exchange.
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Affiliation(s)
- Tommy F Tashjian
- From the Department of Biology, Northeastern University, Boston, Massachusetts 02115
| | - Claudia Danilowicz
- the Department of Physics, Harvard University, Cambridge, Massachusetts 02138, and
| | - Anne-Elizabeth Molza
- the Laboratoire de Biochimie Théorique, CNRS UPR9080 and Université Paris Diderot, IBPC, 75005 Paris, France
| | - Brian H Nguyen
- From the Department of Biology, Northeastern University, Boston, Massachusetts 02115
| | - Chantal Prévost
- the Laboratoire de Biochimie Théorique, CNRS UPR9080 and Université Paris Diderot, IBPC, 75005 Paris, France
| | - Mara Prentiss
- the Department of Physics, Harvard University, Cambridge, Massachusetts 02138, and
| | - Veronica G Godoy
- From the Department of Biology, Northeastern University, Boston, Massachusetts 02115,
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11
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TIRF-Based Single-Molecule Detection of the RecA Presynaptic Filament Dynamics. Methods Enzymol 2018; 600:233-253. [PMID: 29458760 DOI: 10.1016/bs.mie.2017.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RecA is a key protein in homologous DNA repair process. On a single-stranded (ss) DNA, which appears as an intermediate structure at a double-strand break site, RecA forms a kilobase-long presynaptic filament that mediates homology search and strand exchange reaction. RecA requires adenosine triphosphate as a cofactor that confers dynamic features to the filament such as nucleation, end-dependent growth and disassembly, scaffold shift along the ssDNA, and conformational change. Due to the complexity of the dynamics, detailed molecular mechanisms of functioning presynaptic filament have been characterized only recently after the advent of single-molecule techniques that allowed real-time observation of each kinetic process. In this chapter, single-molecule fluorescence resonance energy transfer assays, which revealed detailed molecular pictures of the presynaptic filament dynamics, will be discussed.
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12
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Jaszczur M, Bertram JG, Robinson A, van Oijen AM, Woodgate R, Cox MM, Goodman MF. Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword. Biochemistry 2016; 55:2309-18. [PMID: 27043933 DOI: 10.1021/acs.biochem.6b00117] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1953, the year of Watson and Crick, bore witness to a less acclaimed yet highly influential discovery. Jean Weigle demonstrated that upon infection of Escherichia coli, λ phage deactivated by UV radiation, and thus unable to form progeny, could be reactivated by irradiation of the bacterial host. Evelyn Witkin and Miroslav Radman later revealed the presence of the SOS regulon. The more than 40 regulon genes are repressed by LexA protein and induced by the coproteolytic cleavage of LexA, catalyzed by RecA protein bound to single-stranded DNA, the RecA* nucleoprotein filament. Several SOS-induced proteins are engaged in repairing both cellular and extracellular damaged DNA. There's no "free lunch", however, because error-free repair is accompanied by error-prone translesion DNA synthesis (TLS), involving E. coli DNA polymerase V (UmuD'2C) and RecA*. This review describes the biochemical mechanisms of pol V-mediated TLS. pol V is active only as a mutasomal complex, pol V Mut = UmuD'2C-RecA-ATP. RecA* donates a single RecA subunit to pol V. We highlight three recent insights. (1) pol V Mut has an intrinsic DNA-dependent ATPase activity that governs polymerase binding and dissociation from DNA. (2) Active and inactive states of pol V Mut are determined at least in part by the distinct interactions between RecA and UmuC. (3) pol V is activated by RecA*, not at a blocked replisome, but at the inner cell membrane.
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Affiliation(s)
- Malgorzata Jaszczur
- Department of Biological Sciences, University of Southern California , Los Angeles, California 90089-0371, United States
| | - Jeffrey G Bertram
- Department of Biological Sciences, University of Southern California , Los Angeles, California 90089-0371, United States
| | - Andrew Robinson
- School of Chemistry, University of Wollongong , Wollongong, Australia
| | | | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health , Rockville, Maryland 20850, United States
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California , Los Angeles, California 90089-0371, United States.,Department of Chemistry, University of Southern California , Los Angeles, California 90089-1062, United States
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13
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Shi C, Shang F, Zhou M, Zhang P, Wang Y, Ma C. Triggered isothermal PCR by denaturation bubble-mediated strand exchange amplification. Chem Commun (Camb) 2016; 52:11551-4. [DOI: 10.1039/c6cc05906f] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here, we introduced the concept of strand exchange amplification (SEA) mediated by denaturation bubbles.
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Affiliation(s)
- Chao Shi
- College of Life Sciences
- Qingdao University
- Qingdao
- P. R. China
| | - Fanjin Shang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Meiling Zhou
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Pansong Zhang
- College of Chemical Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
| | - Yifan Wang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Cuiping Ma
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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14
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Gruber AJ, Erdem AL, Sabat G, Karata K, Jaszczur MM, Vo DD, Olsen TM, Woodgate R, Goodman MF, Cox MM. A RecA protein surface required for activation of DNA polymerase V. PLoS Genet 2015; 11:e1005066. [PMID: 25811184 PMCID: PMC4374754 DOI: 10.1371/journal.pgen.1005066] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/11/2015] [Indexed: 11/25/2022] Open
Abstract
DNA polymerase V (pol V) of Escherichia coli is a translesion DNA polymerase responsible for most of the mutagenesis observed during the SOS response. Pol V is activated by transfer of a RecA subunit from the 3'-proximal end of a RecA nucleoprotein filament to form a functional complex called DNA polymerase V Mutasome (pol V Mut). We identify a RecA surface, defined by residues 112-117, that either directly interacts with or is in very close proximity to amino acid residues on two distinct surfaces of the UmuC subunit of pol V. One of these surfaces is uniquely prominent in the active pol V Mut. Several conformational states are populated in the inactive and active complexes of RecA with pol V. The RecA D112R and RecA D112R N113R double mutant proteins exhibit successively reduced capacity for pol V activation. The double mutant RecA is specifically defective in the ATP binding step of the activation pathway. Unlike the classic non-mutable RecA S117F (recA1730), the RecA D112R N113R variant exhibits no defect in filament formation on DNA and promotes all other RecA activities efficiently. An important pol V activation surface of RecA protein is thus centered in a region encompassing amino acid residues 112, 113, and 117, a surface exposed at the 3'-proximal end of a RecA filament. The same RecA surface is not utilized in the RecA activation of the homologous and highly mutagenic RumA'2B polymerase encoded by the integrating-conjugative element (ICE) R391, indicating a lack of structural conservation between the two systems. The RecA D112R N113R protein represents a new separation of function mutant, proficient in all RecA functions except SOS mutagenesis.
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Affiliation(s)
- Angela J Gruber
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Aysen L Erdem
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California, United States of America
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kiyonobu Karata
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Malgorzata M Jaszczur
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California, United States of America
| | - Dan D Vo
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California, United States of America
| | - Tayla M Olsen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California, United States of America
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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15
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DNA transport across the outer and inner membranes of naturally transformable Vibrio cholerae is spatially but not temporally coupled. mBio 2014; 5:mBio.01409-14. [PMID: 25139903 PMCID: PMC4147865 DOI: 10.1128/mbio.01409-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The physiological state of natural competence for transformation allows certain bacteria to take up free DNA from the environment and to recombine such newly acquired DNA into their chromosomes. However, even though conserved components that are required to undergo natural transformation have been identified in several naturally competent bacteria, our knowledge of the underlying mechanisms of the DNA uptake process remains very limited. To better understand these mechanisms, we investigated the competence-mediated DNA transport in the naturally transformable pathogen Vibrio cholerae. Previously, we used a cell biology-based approach to experimentally address an existing hypothesis, which suggested the competence protein ComEA plays a role in the DNA uptake process across the outer membrane of Gram-negative bacteria. Here, we extended this knowledge by investigating the dynamics of DNA translocation across both membranes. More precisely, we indirectly visualized the transfer of the external DNA from outside the cell into the periplasm followed by the shuttling of the DNA into the cytoplasm. Based on these data, we conclude that for V. cholerae, the DNA translocation across the outer and inner membranes is spatially but not temporally coupled. As a mode of horizontal gene transfer, natural competence for transformation has contributed substantially to the plasticity of genomes and to bacterial evolution. Natural competence is often a tightly regulated process and is induced by diverse environmental cues. This is in contrast to the mechanistic aspects of the DNA translocation event, which are most likely conserved among naturally transformable bacteria. However, the DNA uptake process is still not well understood. We therefore investigated how external DNA reaches the cytosol of the naturally transformable bacterium V. cholerae. More specifically, we provide evidence that the DNA translocation across the membranes is spatially but not temporally coupled. We hypothesize that this model also applies to other competent Gram-negative bacteria and that our study contributes to the general understanding of this important biological process.
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16
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Qiu Y, Antony E, Doganay S, Koh HR, Lohman TM, Myong S. Srs2 prevents Rad51 filament formation by repetitive motion on DNA. Nat Commun 2014; 4:2281. [PMID: 23939144 DOI: 10.1038/ncomms3281] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/09/2013] [Indexed: 11/09/2022] Open
Abstract
Srs2 dismantles presynaptic Rad51 filaments and prevents its re-formation as an anti-recombinase. However, the molecular mechanism by which Srs2 accomplishes these tasks remains unclear. Here we report a single-molecule fluorescence study of the dynamics of Rad51 filament formation and its disruption by Srs2. Rad51 forms filaments on single-stranded DNA by sequential binding of primarily monomers and dimers in a 5'-3' direction. One Rad51 molecule binds to three nucleotides, and six monomers are required to achieve a stable nucleation cluster. Srs2 exhibits ATP-dependent repetitive motion on single-stranded DNA and this activity prevents re-formation of the Rad51 filament. The same activity of Srs2 cannot prevent RecA filament formation, indicating its specificity for Rad51. Srs2's DNA-unwinding activity is greatly suppressed when Rad51 filaments form on duplex DNA. Taken together, our results reveal an exquisite and highly specific mechanism by which Srs2 regulates the Rad51 filament formation.
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Affiliation(s)
- Yupeng Qiu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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17
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Abstract
In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered.
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Affiliation(s)
- Jack D Griffith
- From the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295
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18
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Kim SH, Joo C, Ha T, Kim D. Molecular mechanism of sequence-dependent stability of RecA filament. Nucleic Acids Res 2013; 41:7738-44. [PMID: 23804763 PMCID: PMC3763553 DOI: 10.1093/nar/gkt570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
RecA is a DNA-dependent ATPase and mediates homologous recombination by first forming a filament on a single-stranded (ss) DNA. RecA binds preferentially to TGG repeat sequence, which resembles the recombination hot spot Chi (5′-GCTGGTGG-3′) and is the most frequent pattern (GTG) of the codon usage in Escherichia coli. Because of the highly dynamic nature of RecA filament formation, which consists of filament nucleation, growth and shrinkage, we need experimental approaches that can resolve each of these processes separately to gain detailed insights into the molecular mechanism of sequence preference. By using a single-molecule fluorescence assay, we examined the effect of sequence on individual stages of nucleation, monomer binding and dissociation. We found that RecA does not recognize the Chi sequence as a nucleation site. In contrast, we observed that it is the reduced monomer dissociation that mainly determines the high filament stability on TGG repeats. This sequence dependence of monomer dissociation is well-correlated with that of ATP hydrolysis, suggesting that DNA sequence dictates filament stability through modulation of ATP hydrolysis.
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Affiliation(s)
- Sung Hyun Kim
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea, Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands, Department of Physics and Center for the Physics of Living Cells, Institute for Genomic Biology and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Howard Hughes Medical Institute, Urbana, IL 61801, USA
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19
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Bakhlanova IV, Dudkina AV, Baitin DM. Enzymatic control of homologous recombination and hyperrecombination in Escherichia coli. Mol Biol 2013. [DOI: 10.1134/s0026893313020039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Lia G, Rigato A, Long E, Chagneau C, Le Masson M, Allemand JF, Michel B. RecA-promoted, RecFOR-independent progressive disassembly of replisomes stalled by helicase inactivation. Mol Cell 2012; 49:547-57. [PMID: 23260658 DOI: 10.1016/j.molcel.2012.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/17/2012] [Accepted: 11/16/2012] [Indexed: 11/26/2022]
Abstract
In all organisms, replication impairment is a recognized source of genomic instability, raising an increasing interest in the fate of inactivated replication forks. We used Escherichia coli strains with a temperature-inactivated replicative helicase (DnaB) and in vivo single-molecule microscopy to quantify the detailed molecular processing of stalled replication forks. After helicase inactivation, RecA binds to blocked replication forks and is essential for the rapid release of hPol III. The entire holoenzyme is disrupted little by little, with some components lost in few minutes, while others are stable in 70% of cells for at least 1 hr. Although replisome dissociation is delayed in a recA mutant, it is not affected by RecF or RecO inactivation. RecFOR are required for full RecA filaments formation, and we propose that polymerase clearance can be catalyzed by short, RecFOR-independent RecA filaments. Our results identify a function for the universally conserved, central recombination protein RecA.
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Affiliation(s)
- Giuseppe Lia
- CNRS, Centre de Génétique Moléculaire, UPR3404, Gif-sur-Yvette 91198, France.
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21
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22
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Bell JC, Plank JL, Dombrowski CC, Kowalczykowski SC. Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA. Nature 2012; 491:274-8. [PMID: 23103864 PMCID: PMC4112059 DOI: 10.1038/nature11598] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 09/20/2012] [Indexed: 01/14/2023]
Abstract
Escherichia coli RecA is the defining member of a ubiquitous class of DNA strand exchange proteins that are essential for homologous recombination, a pathway that maintains genomic integrity by repairing broken DNA1. To function, filaments of RecA must nucleate and grow on single-stranded DNA (ssDNA) in direct competition with ssDNA-binding protein (SSB), which rapidly binds and continuously sequesters ssDNA, kinetically blocking RecA assembly2,3. This dynamic self-assembly on a DNA lattice, in competition with another protein, is unique for the RecA-family relative to other filament-forming proteins such as actin and tubulin. The complexity of this process has hindered our understanding of RecA filament assembly because ensemble measurements cannot reliably distinguish between the nucleation and growth phases, despite extensive and diverse attempts2–5. Previous single-molecule assays have measured nucleation and growth of RecA—and its eukaryotic homolog RAD51—on naked dsDNA and ssDNA6–12; however, the template for RecA self-assembly in vivo is SSB-coated ssDNA3. Using single-molecule microscopy, we directly visualized RecA filament assembly on single molecules of SSB-coated ssDNA, simultaneously measuring nucleation and growth. We establish that a dimer of RecA is required for nucleation, followed by growth of the filament through monomer addition, consistent with the finding that nucleation, but not growth, is modulated by nucleotide and magnesium ion cofactors. Filament growth is bidirectional, albeit faster in the 5′→3′ direction. Both nucleation and growth are repressed at physiological conditions, highlighting the essential role of recombination mediators in potentiating assembly in vivo. We define a two-step kinetic mechanism where RecA nucleates on transiently exposed ssDNA during SSB sliding and/or partial dissociation (i.e., DNA unwrapping) and then grows. We further demonstrate that the recombination mediator protein pair, RecOR, accelerates both RecA nucleation and filament growth, and that introduction of RecF further stimulates RecA nucleation.
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Affiliation(s)
- Jason C Bell
- Department of Microbiology, University of California, Davis, California 95616, USA
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23
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Morimatsu K, Wu Y, Kowalczykowski SC. RecFOR proteins target RecA protein to a DNA gap with either DNA or RNA at the 5' terminus: implication for repair of stalled replication forks. J Biol Chem 2012; 287:35621-35630. [PMID: 22902627 DOI: 10.1074/jbc.m112.397034] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The repair of single-stranded gaps in duplex DNA by homologous recombination requires the proteins of the RecF pathway. The assembly of RecA protein onto gapped DNA (gDNA) that is complexed with the single-stranded DNA-binding protein is accelerated by the RecF, RecO, and RecR (RecFOR) proteins. Here, we show the RecFOR proteins specifically target RecA protein to gDNA even in the presence of a thousand-fold excess of single-stranded DNA (ssDNA). The binding constant of RecF protein, in the presence of the RecOR proteins, to the junction of ssDNA and dsDNA within a gap is 1-2 nm, suggesting that a few RecF molecules in the cell are sufficient to recognize gDNA. We also found that the nucleation of a RecA filament on gDNA in the presence of the RecFOR proteins occurs at a faster rate than filament elongation, resulting in a RecA nucleoprotein filament on ssDNA for 1000-2000 nucleotides downstream (5' → 3') of the junction with duplex DNA. Thus, RecA loading by RecFOR is localized to a region close to a junction. RecFOR proteins also recognize RNA at the 5'-end of an RNA-DNA junction within an ssDNA gap, which is compatible with their role in the repair of lagging strand gaps at stalled replication forks.
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Affiliation(s)
- Katsumi Morimatsu
- Department of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Yun Wu
- Department of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Stephen C Kowalczykowski
- Department of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616.
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24
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Fagerburg MV, Schauer GD, Thickman KR, Bianco PR, Khan SA, Leuba SH, Anand SP. PcrA-mediated disruption of RecA nucleoprotein filaments--essential role of the ATPase activity of RecA. Nucleic Acids Res 2012; 40:8416-24. [PMID: 22743269 PMCID: PMC3458574 DOI: 10.1093/nar/gks641] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The essential DNA helicase, PcrA, regulates recombination by displacing the recombinase RecA from the DNA. The nucleotide-bound state of RecA determines the stability of its nucleoprotein filaments. Using single-molecule fluorescence approaches, we demonstrate that RecA displacement by a translocating PcrA requires the ATPase activity of the recombinase. We also show that in a ‘head-on collision’ between a polymerizing RecA filament and a translocating PcrA, the RecA K72R ATPase mutant, but not wild-type RecA, arrests helicase translocation. Our findings demonstrate that translocation of PcrA is not sufficient to displace RecA from the DNA and assigns an essential role for the ATPase activity of RecA in helicase-mediated disruption of its filaments.
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Affiliation(s)
- Matt V Fagerburg
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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25
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Jang S, Sandler SJ, Harshey RM. Mu insertions are repaired by the double-strand break repair pathway of Escherichia coli. PLoS Genet 2012; 8:e1002642. [PMID: 22511883 PMCID: PMC3325207 DOI: 10.1371/journal.pgen.1002642] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 02/22/2012] [Indexed: 11/21/2022] Open
Abstract
Mu is both a transposable element and a temperate bacteriophage. During lytic growth, it amplifies its genome by replicative transposition. During infection, it integrates into the Escherichia coli chromosome through a mechanism not requiring extensive DNA replication. In the latter pathway, the transposition intermediate is repaired by transposase-mediated resecting of the 5′ flaps attached to the ends of the incoming Mu genome, followed by filling the remaining 5 bp gaps at each end of the Mu insertion. It is widely assumed that the gaps are repaired by a gap-filling host polymerase. Using the E. coli Keio Collection to screen for mutants defective in recovery of stable Mu insertions, we show in this study that the gaps are repaired by the machinery responsible for the repair of double-strand breaks in E. coli—the replication restart proteins PriA-DnaT and homologous recombination proteins RecABC. We discuss alternate models for recombinational repair of the Mu gaps. Transposon activity shapes genome structure and evolution. The movement of these elements generates target site duplications as a result of staggered cuts in the target made initially by the transposase. For replicative transposons, the single-stranded gaps generated after the initial strand transfer event are filled by target-primed replication. However, the majority of known transposable elements transpose by a non-replicative mechanism. Despite a wealth of information available for the mechanism of transposase action, little is known about how the cell repairs gaps left in the wake of transposition of these majority elements. Phage Mu is unique in using both replicative and non-replicative modes of transposition. Our study finds that during its non-replicative pathway, the gaps created by Mu insertion are repaired by the primary machinery for double-strand break repair in E. coli, not by gap-filling polymerases as previously thought. This first report of specific host processes involved in repair of transposon insertions in bacteria is likely to have a broad significance, given also that double-strand break repair pathways have been implicated in repair of the retroviral and Line retroelement insertions.
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Affiliation(s)
- Sooin Jang
- Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Steven J. Sandler
- Department of Microbiology, Morill Science Center, University of Massachusetts at Amherst, Amherst, Massachusetts, United States of America
| | - Rasika M. Harshey
- Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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26
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Kuzminov A. Homologous Recombination-Experimental Systems, Analysis, and Significance. EcoSal Plus 2011; 4:10.1128/ecosalplus.7.2.6. [PMID: 26442506 PMCID: PMC4190071 DOI: 10.1128/ecosalplus.7.2.6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Indexed: 12/30/2022]
Abstract
Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in Escherichia coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange), and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy.
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Liu J, Ehmsen KT, Heyer WD, Morrical SW. Presynaptic filament dynamics in homologous recombination and DNA repair. Crit Rev Biochem Mol Biol 2011; 46:240-70. [PMID: 21599536 DOI: 10.3109/10409238.2011.576007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Homologous recombination (HR) is an essential genome stability mechanism used for high-fidelity repair of DNA double-strand breaks and for the recovery of stalled or collapsed DNA replication forks. The crucial homology search and DNA strand exchange steps of HR are catalyzed by presynaptic filaments-helical filaments of a recombinase enzyme bound to single-stranded DNA (ssDNA). Presynaptic filaments are fundamentally dynamic structures, the assembly, catalytic turnover, and disassembly of which must be closely coordinated with other elements of the DNA recombination, repair, and replication machinery in order for genome maintenance functions to be effective. Here, we reviewed the major dynamic elements controlling the assembly, activity, and disassembly of presynaptic filaments; some intrinsic such as recombinase ATP-binding and hydrolytic activities, others extrinsic such as ssDNA-binding proteins, mediator proteins, and DNA motor proteins. We examined dynamic behavior on multiple levels, including atomic- and filament-level structural changes associated with ATP binding and hydrolysis as evidenced in crystal structures, as well as subunit binding and dissociation events driven by intrinsic and extrinsic factors. We examined the biochemical properties of recombination proteins from four model systems (T4 phage, Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens), demonstrating how their properties are tailored for the context-specific requirements in these diverse species. We proposed that the presynaptic filament has evolved to rely on multiple external factors for increased multilevel regulation of HR processes in genomes with greater structural and sequence complexity.
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Affiliation(s)
- Jie Liu
- Departments of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA, USA
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28
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Nevinsky GA. Structural, thermodynamic, and kinetic basis for the activities of some nucleic acid repair enzymes. J Mol Recognit 2011; 24:656-77. [PMID: 21584877 DOI: 10.1002/jmr.1096] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
X-ray structural analysis provides no quantitative estimate of the relative contribution of specific and nonspecific or strong and weak interactions to the total affinity of enzymes for nucleic acids. We have shown that the interaction between enzymes and long nucleic acids at the molecular level can be successfully analyzed by the method of stepwise increase in ligand complexity (SILC). In the present review we summarize our studies of human uracil DNA glycosylase and apurinic/apyrimidinic endonuclease, E. coli 8-oxoguanine DNA glycosylase and RecA protein using the SILC approach. The relative contribution of structural (X-ray analysis data), thermodynamic, and catalytic factors to the discrimination of specific and nonspecific DNA by these enzymes at the stages of complex formation, the following changes in DNA and enzyme conformations and especially the catalysis of the reactions is discussed.
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Affiliation(s)
- Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 63009, Russia.
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29
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Dudkina AV, Schvetsov AV, Bakhlanova IV, Baitin DM. Change of filamentation dynamics of RecA protein induced by D112R Amino acid substitution or ATP to dATP replacement; results in filament resistance to RecX protein action. Mol Biol 2011. [DOI: 10.1134/s0026893311030046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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30
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Nevinsky GA. Main factors providing specificity of repair enzymes. BIOCHEMISTRY (MOSCOW) 2011; 76:94-117. [PMID: 21568843 DOI: 10.1134/s0006297911010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Specific and nonspecific DNA complex formation with human uracil-DNA glycosylase, 8-oxoguanine-DNA glycosylase, and apurine/apyrimidine endonuclease, as well as with E. coli 8-oxoguanine-DNA glycosylase and RecA protein was analyzed using the method of stepwise increase in DNA-ligand complexity. It is shown that high affinity of these enzymes to any DNA (10(-4)-10(-8) M) is provided by a large number of weak additive contacts mainly with DNA internucleoside phosphate groups and in a less degree with bases of nucleotide links "covered" by protein globules. Enzyme interactions with specific DNA links are comparable in efficiency with weak unspecific contacts and provide only for one-two orders of affinity (10(-1)-10(-2) M), but these contacts are extremely important at stages of DNA and enzyme structural adaptation and catalysis proper. Only in the case of specific DNA individual for each enzyme alterations in DNA structure provide for efficient adjustment of reacting enzyme atoms and DNA orbitals with accuracy up to 10-15° and, as a result, for high reaction rate. Upon transition from nonspecific to specific DNA, reaction rate (k(cat)) increases by 4-8 orders of magnitude. Thus, stages of DNA and enzyme structural adaptation as well as catalysis proper are the basis of specificity of repair enzymes.
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Affiliation(s)
- G A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
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31
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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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Murayama Y, Tsutsui Y, Iwasaki H. The fission yeast meiosis-specific Dmc1 recombinase mediates formation and branch migration of Holliday junctions by preferentially promoting strand exchange in a direction opposite to that of Rad51. Genes Dev 2011; 25:516-27. [PMID: 21363965 DOI: 10.1101/gad.1997511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Homologous recombination proceeds via the formation of several intermediates including Holliday junctions (HJs), which are important for creating crossover products. DNA strand exchange is a core reaction that produces these intermediates that is directly catalyzed by RecA family recombinases, of which there are two types in eukaryotes: universal Rad51 and meiosis-specific Dmc1. We demonstrated previously that Rad51 promotes four-strand exchange, mimicking the formation and branch migration of HJs. Here we show that Dmc1 from fission yeast has a similar activity, which requires ATP hydrolysis and is independent of an absolute requirement for the Swi5-Sfr1 complex. These features are critically different from three-strand exchange mediated by Dmc1, but similar to those of four-strand exchange mediated by Rad51, suggesting that strand exchange reactions between duplex-duplex and single-duplex DNAs are mechanistically different. Interestingly, despite similarities in protein structure and in reaction features, the preferential polarities of Dmc1 and Rad51 strand exchange are different (Dmc1 promotes exchange in the 5'-to-3' direction and Rad51 promotes exchange in the 3'-to-5' direction relative to the ssDNA region of the DNA substrate). The significance of the Dmc1 polarity is discussed within the context of the necessity for crossover production.
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Affiliation(s)
- Yasuto Murayama
- Department of Life Science, School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
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The RecA/RAD51 protein drives migration of Holliday junctions via polymerization on DNA. Proc Natl Acad Sci U S A 2011; 108:6432-7. [PMID: 21464277 DOI: 10.1073/pnas.1016072108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Holliday junction (HJ), a cross-shaped structure that physically links the two DNA helices, is a key intermediate in homologous recombination, DNA repair, and replication. Several helicase-like proteins are known to bind HJs and promote their branch migration (BM) by translocating along DNA at the expense of ATP hydrolysis. Surprisingly, the bacterial recombinase protein RecA and its eukaryotic homologue Rad51 also promote BM of HJs despite the fact they do not bind HJs preferentially and do not translocate along DNA. RecA/Rad51 plays a key role in DNA double-stranded break repair and homologous recombination. RecA/Rad51 binds to ssDNA and forms contiguous filaments that promote the search for homologous DNA sequences and DNA strand exchange. The mechanism of BM promoted by RecA/RAD51 is unknown. Here, we demonstrate that cycles of RecA/Rad51 polymerization and dissociation coupled with ATP hydrolysis drives the BM of HJs.
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Britt RL, Chitteni-Pattu S, Page AN, Cox MM. RecA K72R filament formation defects reveal an oligomeric RecA species involved in filament extension. J Biol Chem 2011; 286:7830-7840. [PMID: 21193798 PMCID: PMC3048670 DOI: 10.1074/jbc.m110.194407] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/21/2010] [Indexed: 11/06/2022] Open
Abstract
Using an ensemble approach, we demonstrate that an oligomeric RecA species is required for the extension phase of RecA filament formation. The RecA K72R mutant protein can bind but not hydrolyze ATP or dATP. When mixed with other RecA variants, RecA K72R causes a drop in the rate of ATP hydrolysis and has been used to study disassembly of hydrolysis-proficient RecA protein filaments. RecA K72R filaments do not form in the presence of ATP but do so when dATP is provided. We demonstrate that in the presence of ATP, RecA K72R is defective for extension of RecA filaments on DNA. This defect is partially rescued when the mutant protein is mixed with sufficient levels of wild type RecA protein. Functional extension complexes form most readily when wild type RecA is in excess of RecA K72R. Thus, RecA K72R inhibits hydrolysis-proficient RecA proteins by interacting with them in solution and preventing the extension phase of filament assembly.
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Affiliation(s)
- Rachel L Britt
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Sindhu Chitteni-Pattu
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Asher N Page
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Michael M Cox
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706.
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Gruenig MC, Stohl EA, Chitteni-Pattu S, Seifert HS, Cox MM. Less is more: Neisseria gonorrhoeae RecX protein stimulates recombination by inhibiting RecA. J Biol Chem 2010; 285:37188-97. [PMID: 20851893 PMCID: PMC2988325 DOI: 10.1074/jbc.m110.171967] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 09/12/2010] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli RecX (RecX(Ec)) is a negative regulator of RecA activities both in the bacterial cell and in vitro. In contrast, the Neisseria gonorrhoeae RecX protein (RecX(Ng)) enhances all RecA-related processes in N. gonorrhoeae. Surprisingly, the RecX(Ng) protein is not a RecA protein activator in vitro. Instead, RecX(Ng) is a much more potent inhibitor of all RecA(Ng) and RecA(Ec) activities than is the E. coli RecX ortholog. A series of RecX(Ng) mutant proteins representing a gradient of functional deficiencies provide a direct correlation between RecA(Ng) inhibition in vitro and the enhancement of RecA(Ng) function in N. gonorrhoeae. Unlike RecX(Ec), RecX(Ng) does not simply cap the growing ends of RecA filaments, but it directly facilitates a more rapid RecA filament disassembly. Thus, in N. gonorrhoeae, recombinational processes are facilitated by RecX(Ng) protein-mediated limitations on RecA(Ng) filament presence and/or length to achieve maximal function.
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Affiliation(s)
- Marielle C Gruenig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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36
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Li BS, Goh MC. Direct evidence of the role of ATPγS in the binding of single-stranded binding protein (Escherichia coli) and RecA to single-stranded DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14755-14758. [PMID: 20722443 DOI: 10.1021/la102347b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
To gain insight into the influence of ATPγS on the competitive binding of RecA and single-stranded binding protein (SSB) on single-stranded DNA (ssDNA), AFM imaging was used to examine the three-dimensional structures of the different complexes formed by the binding of the two proteins on ssDNA in the presence and absence of ATPγS. In the presence of ATPγS, RecA attaches to ssDNA, displacing SSB, to form continuous binding regions that caused considerable elongation of the strand. When ATPγS is absent, RecA could not compete with SSB and only binds at a few sites that correspond to the vacancy in ssDNA left when SSB unbinds. These results provide direct evidence that, while SSB binding affinity to DNA is substantially higher than that of RecA, the presence of ATPγS is sufficient to alter the events and enable RecA coating of DNA.
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Affiliation(s)
- Bing Shi Li
- Department of Chemistry and Institute for Optical Sciences, University of Toronto, Toronto, Ontario, M5S 3H6 Canada.
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37
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Patel M, Jiang Q, Woodgate R, Cox MM, Goodman MF. A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev Biochem Mol Biol 2010; 45:171-84. [PMID: 20441441 DOI: 10.3109/10409238.2010.480968] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In Escherichia coli, cell survival and genomic stability after UV radiation depends on repair mechanisms induced as part of the SOS response to DNA damage. The early phase of the SOS response is mostly dominated by accurate DNA repair, while the later phase is characterized with elevated mutation levels caused by error-prone DNA replication. SOS mutagenesis is largely the result of the action of DNA polymerase V (pol V), which has the ability to insert nucleotides opposite various DNA lesions in a process termed translesion DNA synthesis (TLS). Pol V is a low-fidelity polymerase that is composed of UmuD'(2)C and is encoded by the umuDC operon. Pol V is strictly regulated in the cell so as to avoid genomic mutation overload. RecA nucleoprotein filaments (RecA*), formed by RecA binding to single-stranded DNA with ATP, are essential for pol V-catalyzed TLS both in vivo and in vitro. This review focuses on recent studies addressing the protein composition of active DNA polymerase V, and the role of RecA protein in activating this enzyme. Based on unforeseen properties of RecA*, we describe a new model for pol V-catalyzed SOS-induced mutagenesis.
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Affiliation(s)
- Meghna Patel
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
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38
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Hinz JM. Role of homologous recombination in DNA interstrand crosslink repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:582-603. [PMID: 20658649 DOI: 10.1002/em.20577] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Homologous recombination repair (HRR) encompasses mechanisms that employ homologous DNA sequences as templates for repair or tolerance of a wide range of DNA lesions that inhibit DNA replication in S phase. Arguably the most imposing of these DNA lesions is that of the interstrand crosslink (ICL), consisting of a covalently attached chemical bridge between opposing DNA strands. ICL repair requires the coordinated activities of HRR and a number of proteins from other DNA repair and damage response systems, including nucleotide excision repair, base excision repair, mismatch repair, and translesion DNA synthesis (TLS). Interestingly, different organisms favor alternative methods of HRR in the ICL repair process. E. coli perform ICL repair using a homology-driven damage bypass mechanism analogous to daughter strand gap repair. Eukaryotes from yeast to humans initiate ICL repair primarily during DNA replication, relying on HRR activity to restart broken replication forks associated with double-strand break intermediates induced by nucleolytic activities of other excision repair factors. Higher eukaryotes also employ several additional factors, including members of the Fanconi anemia damage-response network, which further promote replication-associated ICL repair through the activation and coordination of various DNA excision repair, TLS, and HRR proteins. This review focuses on the proteins and general mechanisms of HRR associated with ICL repair in different model organisms.
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Affiliation(s)
- John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
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39
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Carra C, Cucinotta FA. Binding selectivity of RecA to a single stranded DNA, a computational approach. J Mol Model 2010; 17:133-50. [PMID: 20386943 DOI: 10.1007/s00894-010-0694-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 02/23/2010] [Indexed: 11/29/2022]
Abstract
Homologous recombination (HR) is the major DNA double strand break repair pathway which maintains the genomic integrity. It is fundamental for the survivability and functionality of all organisms. One of the initial steps in HR is the formation of the nucleoprotein filament composed by a single stranded DNA chain surrounded by the recombinases protein. The filament orchestrates the search for an undamaged homologue, as a template for the repair process. Our theoretical study was aimed at elucidating the selectivity of the interaction between a monomer of the recombinases enzyme in the Escherichia coli, EcRecA, the bacterial homologue of human Rad51, with a series of oligonucleotides of nine bases length. The complex, equilibrated for 20 ns with Langevian dynamics, was inserted in a periodic box with a 8 Å buffer of water molecules explicitly described by the TIP3P model. The absolute binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann (PB) and the generalized Born (GB) solvent accessible surface area, using the MM-PB(GB)SA model. The solute entropic contribution is also calculated by normal mode analysis. The results underline how a significant contribution of the binding free energy is due to the interaction with the Arg196, a critical amino acid for the activity of the enzyme. The study revealed how the binding affinity of EcRecA is significantly higher toward dT₉ rather than dA₉, as expected from the experimental results.
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Affiliation(s)
- Claudio Carra
- Universities Space Research Association, 2101 NASA Parkway, Houston, TX 77058, USA.
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40
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Li BS, Goh MC. Direct visualization of the formation and structure of RecA/dsDNA complexes. Micron 2010; 41:227-31. [DOI: 10.1016/j.micron.2009.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 10/26/2009] [Indexed: 10/20/2022]
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41
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Carra C, Cucinotta FA. Binding Sites of theE. ColiDNA Recombinase Protein to the ssDNA: A Computational Study. J Biomol Struct Dyn 2010; 27:407-28. [DOI: 10.1080/07391102.2010.10507327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Mani A, Braslavsky I, Arbel-Goren R, Stavans J. Caught in the act: the lifetime of synaptic intermediates during the search for homology on DNA. Nucleic Acids Res 2009; 38:2036-43. [PMID: 20044347 PMCID: PMC2847238 DOI: 10.1093/nar/gkp1177] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Homologous recombination plays pivotal roles in DNA repair and in the generation of genetic diversity. To locate homologous target sequences at which strand exchange can occur within a timescale that a cell’s biology demands, a single-stranded DNA-recombinase complex must search among a large number of sequences on a genome by forming synapses with chromosomal segments of DNA. A key element in the search is the time it takes for the two sequences of DNA to be compared, i.e. the synapse lifetime. Here, we visualize for the first time fluorescently tagged individual synapses formed by RecA, a prokaryotic recombinase, and measure their lifetime as a function of synapse length and differences in sequence between the participating DNAs. Surprisingly, lifetimes can be ∼10 s long when the DNAs are fully heterologous, and much longer for partial homology, consistently with ensemble FRET measurements. Synapse lifetime increases rapidly as the length of a region of full homology at either the 3′- or 5′-ends of the invading single-stranded DNA increases above 30 bases. A few mismatches can reduce dramatically the lifetime of synapses formed with nearly homologous DNAs. These results suggest the need for facilitated homology search mechanisms to locate homology successfully within the timescales observed in vivo.
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Affiliation(s)
- Adam Mani
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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43
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Britt RL, Haruta N, Lusetti SL, Chitteni-Pattu S, Inman RB, Cox MM. Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange. J Biol Chem 2009; 285:3211-26. [PMID: 19910465 DOI: 10.1074/jbc.m109.028951] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Disassembly of RecA protein subunits from a RecA filament has long been known to occur during DNA strand exchange, although its importance to this process has been controversial. An Escherichia coli RecA E38K/DeltaC17 double mutant protein displays a unique and pH-dependent mutational separation of DNA pairing and extended DNA strand exchange. Single strand DNA-dependent ATP hydrolysis is catalyzed by this mutant protein nearly normally from pH 6 to 8.5. It will also form filaments on DNA and promote DNA pairing. However, below pH 7.3, ATP hydrolysis is completely uncoupled from extended DNA strand exchange. The products of extended DNA strand exchange do not form. At the lower pH values, disassembly of RecA E38K/DeltaC17 filaments is strongly suppressed, even when homologous DNAs are paired and available for extended DNA strand exchange. Disassembly of RecA E38K/DeltaC17 filaments improves at pH 8.5, whereas complete DNA strand exchange is also restored. Under these sets of conditions, a tight correlation between filament disassembly and completion of DNA strand exchange is observed. This correlation provides evidence that RecA filament disassembly plays a major role in, and may be required for, DNA strand exchange. A requirement for RecA filament disassembly in DNA strand exchange has a variety of ramifications for the current models linking ATP hydrolysis to DNA strand exchange.
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Affiliation(s)
- Rachel L Britt
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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44
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van Loenhout MTJ, van der Heijden T, Kanaar R, Wyman C, Dekker C. Dynamics of RecA filaments on single-stranded DNA. Nucleic Acids Res 2009; 37:4089-99. [PMID: 19429893 PMCID: PMC2709578 DOI: 10.1093/nar/gkp326] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RecA, the key protein in homologous recombination, performs its actions as a helical filament on single-stranded DNA (ssDNA). ATP hydrolysis makes the RecA-ssDNA filament dynamic and is essential for successful recombination. RecA has been studied extensively by single-molecule techniques on double-stranded DNA (dsDNA). Here we directly probe the structure and kinetics of RecA interaction with its biologically most relevant substrate, long ssDNA molecules. We find that RecA ATPase activity is required for the formation of long continuous filaments on ssDNA. These filaments both nucleate and extend with a multimeric unit as indicated by the Hill coefficient of 5.4 for filament nucleation. Disassembly rates of RecA from ssDNA decrease with applied stretching force, corresponding to a mechanism where protein-induced stretching of the ssDNA aids in the disassembly. Finally, we show that RecA-ssDNA filaments can reversibly interconvert between an extended, ATP-bound, and a compressed, ADP-bound state. Taken together, our results demonstrate that ATP hydrolysis has a major influence on the structure and state of RecA filaments on ssDNA.
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Affiliation(s)
- Marijn T J van Loenhout
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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45
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RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev 2009; 72:642-71, Table of Contents. [PMID: 19052323 DOI: 10.1128/mmbr.00020-08] [Citation(s) in RCA: 404] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The RecBCD enzyme of Escherichia coli is a helicase-nuclease that initiates the repair of double-stranded DNA breaks by homologous recombination. It also degrades linear double-stranded DNA, protecting the bacteria from phages and extraneous chromosomal DNA. The RecBCD enzyme is, however, regulated by a cis-acting DNA sequence known as Chi (crossover hotspot instigator) that activates its recombination-promoting functions. Interaction with Chi causes an attenuation of the RecBCD enzyme's vigorous nuclease activity, switches the polarity of the attenuated nuclease activity to the 5' strand, changes the operation of its motor subunits, and instructs the enzyme to begin loading the RecA protein onto the resultant Chi-containing single-stranded DNA. This enzyme is a prototypical example of a molecular machine: the protein architecture incorporates several autonomous functional domains that interact with each other to produce a complex, sequence-regulated, DNA-processing machine. In this review, we discuss the biochemical mechanism of the RecBCD enzyme with particular emphasis on new developments relating to the enzyme's structure and DNA translocation mechanism.
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46
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Persky NS, Lovett ST. Mechanisms of Recombination: Lessons fromE. coli. Crit Rev Biochem Mol Biol 2009; 43:347-70. [DOI: 10.1080/10409230802485358] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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48
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Shereda RD, Kozlov AG, Lohman TM, Cox MM, Keck JL. SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 2008; 43:289-318. [PMID: 18937104 PMCID: PMC2583361 DOI: 10.1080/10409230802341296] [Citation(s) in RCA: 406] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When duplex DNA is altered in almost any way (replicated, recombined, or repaired), single strands of DNA are usually intermediates, and single-stranded DNA binding (SSB) proteins are present. These proteins have often been described as inert, protective DNA coatings. Continuing research is demonstrating a far more complex role of SSB that includes the organization and/or mobilization of all aspects of DNA metabolism. Escherichia coli SSB is now known to interact with at least 14 other proteins that include key components of the elaborate systems involved in every aspect of DNA metabolism. Most, if not all, of these interactions are mediated by the amphipathic C-terminus of SSB. In this review, we summarize the extent of the eubacterial SSB interaction network, describe the energetics of interactions with SSB, and highlight the roles of SSB in the process of recombination. Similar themes to those highlighted in this review are evident in all biological systems.
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Affiliation(s)
- Robert D Shereda
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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49
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Baitin DM, Gruenig MC, Cox MM. SSB antagonizes RecX-RecA interaction. J Biol Chem 2008; 283:14198-204. [PMID: 18385131 PMCID: PMC2386935 DOI: 10.1074/jbc.m801511200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 04/01/2008] [Indexed: 11/06/2022] Open
Abstract
The RecX protein of Escherichia coli inhibits the extension of RecA protein filaments on DNA, presumably by binding to and blocking the growing filament end. The direct binding of RecX protein to single-stranded DNA is weak, and previous reports suggested that direct binding to DNA did not explain the effects of RecX. We now demonstrate that elevated concentrations of SSB greatly moderate the effects of RecX protein. High concentrations of the yeast RPA protein have the same effect, suggesting that the effect is not species-specific or even specific to bacterial SSB proteins. A direct SSB-RecX interaction is thus unlikely. We suggest that SSB is blocking access to single-stranded DNA. The evident competition between RecX and SSB implies that the mechanism of RecX action may involve RecX binding to both RecA protein and to DNA. We speculate that the interaction of RecX protein and RecA may enable an enhanced DNA binding by RecX protein. The effects of SSB are increased if the SSB C terminus is removed.
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Affiliation(s)
- Dmitry M Baitin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
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50
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Leuba SH, Anand SP, Harp JM, Khan SA. Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time. Chromosome Res 2008; 16:451-67. [PMID: 18461484 PMCID: PMC2413326 DOI: 10.1007/s10577-008-1235-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many questions in molecular and cellular biology can be reduced to questions about 'who talks to whom, when and how frequently'. Here, we review approaches we have used with single-pair fluorescence resonance energy transfer (spFRET) to follow the motions between two well-placed fluorescent probes to ask similar questions. We describe two systems. We have used a nucleosomal system in which the naked DNA molecule has the acceptor and donor dyes too far apart for FRET to occur whereas the dyes are close enough in the reconstituted nucleosome for FRET. As these individual nucleosomes were tethered on a surface, we could follow dynamics in the repositioning of these two dyes, inferring that nucleosomes stochastically and reversibly open and close. These results imply that most of the DNA on the nucleosome can be sporadically accessible to regulatory proteins and proteins that track the DNA double helix. In the case of following the binding of recombination protein RecA to double-stranded DNA (dsDNA) and the RecA filament displacement by DNA helicase motor PcrA, the dsDNA template is prepared with the two dyes close enough to each other to generate high FRET. Binding of the RecA molecules to form a filament lengthens the dsDNA molecule 1.5-fold and reduces the FRET accordingly. Once added, DNA motor protein helicase PcrA can displace the RecA filament with concomitant return of the DNA molecule to its original B-form and high FRET state. Thus, appropriately placed fluorescent dyes can be used to monitor conformational changes occurring in DNA and or proteins and provide increased sensitivity for investigating dynamic DNA-protein interactions in real time.
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Affiliation(s)
- Sanford H Leuba
- Department of Cell Biology, University of Pittsburgh School of Medicine and Swanson School of Engineering, Petersen Institute of NanoScience and Engineering and University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA.
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