1
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Welikala MU, Butterworth LJ, Behrmann MS, Trakselis MA. Tau mediated coupling between Pol III synthesis and DnaB helicase unwinding helps maintain genomic stability. J Biol Chem 2024:107726. [PMID: 39214305 DOI: 10.1016/j.jbc.2024.107726] [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: 04/10/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
The τ-subunit of the clamp loader complex (CLC) physically interacts with both the DnaB helicase and the polymerase III (Pol III) core α-subunit through Domains IV and V, respectively. This interaction is proposed to help maintain rapid and efficient DNA synthesis rates with high genomic fidelity and plasticity, facilitating enzymatic coupling within the replisome. To test this hypothesis, CRISPR-Cas9 editing was used to create site-directed genomic mutations within the dnaX gene at the C-terminus of τ predicted to interact with the α-subunit of Pol III. Perturbation of the α-τ binding interaction in vivo resulted in cellular and genomic stress markers that included reduced growth rates, fitness, and viabilities. Specifically, dnaX:mut strains showed increased cell filamentation, mutagenesis frequencies, and activated SOS. In situ fluorescence flow cytometry and microscopy quantified large increases in the amount of single-stranded DNA (ssDNA) gaps present. Removal of the C-terminus of τ (I618X) still maintained its interactions with DnaB and stimulated unwinding but lost its interaction with Pol III, resulting in significantly reduced rolling circle DNA synthesis. Intriguingly, dnaX:L635P/D636G had the largest induction of SOS, high mutagenesis, and the most prominent ssDNA gaps, which can be explained by an impaired ability to regulate the unwinding speed of DnaB resulting in a faster rate of in vitro rolling circle DNA replication, inducing replisome decoupling. Therefore, τ stimulated DnaB unwinding and physical coupling with Pol III acts to enforce replisome plasticity to maintain an efficient rate of synthesis and prevent genomic instability.
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Affiliation(s)
- Malisha U Welikala
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA
| | - Lauren J Butterworth
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA
| | - Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348, USA.
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2
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Behrmann M, Perera H, Welikala M, Matthews J, Butterworth L, Trakselis M. Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization. Nucleic Acids Res 2024; 52:6977-6993. [PMID: 38808668 PMCID: PMC11229327 DOI: 10.1093/nar/gkae435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/03/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024] Open
Abstract
The replicative helicase, DnaB, is a central component of the replisome and unwinds duplex DNA coupled with immediate template-dependent DNA synthesis by the polymerase, Pol III. The rate of helicase unwinding is dynamically regulated through structural transitions in the DnaB hexamer between dilated and constricted states. Site-specific mutations in DnaB enforce a faster more constricted conformation that dysregulates unwinding dynamics, causing replisome decoupling that generates excess ssDNA and induces severe cellular stress. This surplus ssDNA can stimulate RecA recruitment to initiate recombinational repair, restart, or activation of the transcriptional SOS response. To better understand the consequences of dysregulated unwinding, we combined targeted genomic dnaB mutations with an inducible RecA filament inhibition strategy to examine the dependencies on RecA in mitigating replisome decoupling phenotypes. Without RecA filamentation, dnaB:mut strains had reduced growth rates, decreased mutagenesis, but a greater burden from endogenous damage. Interestingly, disruption of RecA filamentation in these dnaB:mut strains also reduced cellular filamentation but increased markers of double strand breaks and ssDNA gaps as detected by in situ fluorescence microscopy and FACS assays, TUNEL and PLUG, respectively. Overall, RecA plays a critical role in strain survival by protecting and processing ssDNA gaps caused by dysregulated helicase activity in vivo.
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Affiliation(s)
- Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA
| | - Himasha M Perera
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA
| | - Malisha U Welikala
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA
| | - Jacquelynn E Matthews
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA
| | - Lauren J Butterworth
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA
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3
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Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA. Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication. J Biol Chem 2024; 300:107166. [PMID: 38490435 PMCID: PMC11044049 DOI: 10.1016/j.jbc.2024.107166] [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: 01/10/2024] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader replication factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the Escherichia coli clamp loader at high resolution using cryo-electron microscopy. We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how the clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.
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Affiliation(s)
- Jacob T Landeck
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emily K Norman
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emma L Sedivy
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
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4
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McHenry CS. Life at the replication fork: A scientific and personal journey. J Biol Chem 2024; 300:105658. [PMID: 38219819 PMCID: PMC10850973 DOI: 10.1016/j.jbc.2024.105658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 01/16/2024] Open
Affiliation(s)
- Charles S McHenry
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA.
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5
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Newcomb ESP, Douma LG, Morris LA, Bloom LB. The Escherichia coli clamp loader rapidly remodels SSB on DNA to load clamps. Nucleic Acids Res 2022; 50:12872-12884. [PMID: 36511874 PMCID: PMC9825162 DOI: 10.1093/nar/gkac1169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Single-stranded DNA binding proteins (SSBs) avidly bind ssDNA and yet enzymes that need to act during DNA replication and repair are not generally impeded by SSB, and are often stimulated by SSB. Here, the effects of Escherichia coli SSB on the activities of the DNA polymerase processivity clamp loader were investigated. SSB enhances binding of the clamp loader to DNA by increasing the lifetime on DNA. Clamp loading was measured on DNA substrates that differed in length of ssDNA overhangs to permit SSB binding in different binding modes. Even though SSB binds DNA adjacent to single-stranded/double-stranded DNA junctions where clamps are loaded, the rate of clamp loading on DNA was not affected by SSB on any of the DNA substrates. Direct measurements of the relative timing of DNA-SSB remodeling and enzyme-DNA binding showed that the clamp loader rapidly remodels SSB on DNA such that SSB has little effect on DNA binding rates. However, when SSB was mutated to reduce protein-protein interactions with the clamp loader, clamp loading was inhibited by impeding binding of the clamp loader to DNA. Thus, protein-protein interactions between the clamp loader and SSB facilitate rapid DNA-SSB remodeling to allow rapid clamp loader-DNA binding and clamp loading.
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Affiliation(s)
- Elijah S P Newcomb
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Lauren G Douma
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Leslie A Morris
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Linda B Bloom
- To whom correspondence should be addressed. Tel: +1 352 294 8379; Fax: +1 352 392 2953;
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6
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Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways. DNA Repair (Amst) 2021; 108:103229. [PMID: 34601381 DOI: 10.1016/j.dnarep.2021.103229] [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: 05/03/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
Helicases involved in genomic maintenance are a class of nucleic-acid dependent ATPases that convert the energy of ATP hydrolysis into physical work to execute irreversible steps in DNA replication, repair, and recombination. Prokaryotic helicases provide simple models to understand broadly conserved molecular mechanisms involved in manipulating nucleic acids during genome maintenance. Our understanding of the catalytic properties, mechanisms of regulation, and roles of prokaryotic helicases in DNA metabolism has been assembled through a combination of genetic, biochemical, and structural methods, further refined by single-molecule approaches. Together, these investigations have constructed a framework for understanding the mechanisms that maintain genomic integrity in cells. This review discusses recent single-molecule insights into molecular mechanisms of prokaryotic helicases and translocases.
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7
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Spinks RR, Spenkelink LM, Stratmann SA, Xu ZQ, Stamford NPJ, Brown SE, Dixon NE, Jergic S, van Oijen AM. DnaB helicase dynamics in bacterial DNA replication resolved by single-molecule studies. Nucleic Acids Res 2021; 49:6804-6816. [PMID: 34139009 PMCID: PMC8266626 DOI: 10.1093/nar/gkab493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 01/09/2023] Open
Abstract
In Escherichia coli, the DnaB helicase forms the basis for the assembly of the DNA replication complex. The stability of DnaB at the replication fork is likely important for successful replication initiation and progression. Single-molecule experiments have significantly changed the classical model of highly stable replication machines by showing that components exchange with free molecules from the environment. However, due to technical limitations, accurate assessments of DnaB stability in the context of replication are lacking. Using in vitro fluorescence single-molecule imaging, we visualise DnaB loaded on forked DNA templates. That these helicases are highly stable at replication forks, indicated by their observed dwell time of ∼30 min. Addition of the remaining replication factors results in a single DnaB helicase integrated as part of an active replisome. In contrast to the dynamic behaviour of other replisome components, DnaB is maintained within the replisome for the entirety of the replication process. Interestingly, we observe a transient interaction of additional helicases with the replication fork. This interaction is dependent on the τ subunit of the clamp-loader complex. Collectively, our single-molecule observations solidify the role of the DnaB helicase as the stable anchor of the replisome, but also reveal its capacity for dynamic interactions.
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Affiliation(s)
- Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Sarah A Stratmann
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - N Patrick J Stamford
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Susan E Brown
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia.,Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
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8
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Monachino E, Jergic S, Lewis JS, Xu ZQ, Lo ATY, O'Shea VL, Berger JM, Dixon NE, van Oijen AM. A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome. Mol Cell 2020; 79:140-154.e7. [PMID: 32464091 DOI: 10.1016/j.molcel.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/12/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Recent studies of bacterial DNA replication have led to a picture of the replisome as an entity that freely exchanges DNA polymerases and displays intermittent coupling between the helicase and polymerase(s). Challenging the textbook model of the polymerase holoenzyme acting as a stable complex coordinating the replisome, these observations suggest a role of the helicase as the central organizing hub. We show here that the molecular origin of this newly found plasticity lies in the 500-fold increase in strength of the interaction between the polymerase holoenzyme and the replicative helicase upon association of the primase with the replisome. By combining in vitro ensemble-averaged and single-molecule assays, we demonstrate that this conformational switch operates during replication and promotes recruitment of multiple holoenzymes at the fork. Our observations provide a molecular mechanism for polymerase exchange and offer a revised model for the replication reaction that emphasizes its stochasticity.
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Affiliation(s)
- Enrico Monachino
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747, the Netherlands
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Allen T Y Lo
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Valerie L O'Shea
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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9
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Perera HM, Behrmann MS, Hoang JM, Griffin WC, Trakselis MA. Contacts and context that regulate DNA helicase unwinding and replisome progression. Enzymes 2019; 45:183-223. [PMID: 31627877 DOI: 10.1016/bs.enz.2019.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hexameric DNA helicases involved in the separation of duplex DNA at the replication fork have a universal architecture but have evolved from two separate protein families. The consequences are that the regulation, translocation polarity, strand specificity, and architectural orientation varies between phage/bacteria to that of archaea/eukaryotes. Once assembled and activated for single strand DNA translocation and unwinding, the DNA polymerase couples tightly to the helicase forming a robust replisome complex. However, this helicase-polymerase interaction can be challenged by various forms of endogenous or exogenous agents that can stall the entire replisome or decouple DNA unwinding from synthesis. The consequences of decoupling can be severe, leading to a build-up of ssDNA requiring various pathways for replication fork restart. All told, the hexameric helicase sits prominently at the front of the replisome constantly responding to a variety of obstacles that require transient unwinding/reannealing, traversal of more stable blocks, and alternations in DNA unwinding speed that regulate replisome progression.
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Affiliation(s)
- Himasha M Perera
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Joy M Hoang
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States.
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10
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A quest for coordination among activities at the replisome. Biochem Soc Trans 2019; 47:1067-1075. [PMID: 31395754 DOI: 10.1042/bst20180402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
Faithful DNA replication is required for transmission of the genetic material across generations. The basic mechanisms underlying this process are shared among all organisms: progressive unwinding of the long double-stranded DNA; synthesis of RNA primers; and synthesis of a new DNA chain. These activities are invariably performed by a multi-component machine called the replisome. A detailed description of this molecular machine has been achieved in prokaryotes and phages, with the replication processes in eukaryotes being comparatively less known. However, recent breakthroughs in the in vitro reconstitution of eukaryotic replisomes have resulted in valuable insight into their functions and mechanisms. In conjunction with the developments in eukaryotic replication, an emerging overall view of replisomes as dynamic protein ensembles is coming into fruition. The purpose of this review is to provide an overview of the recent insights into the dynamic nature of the bacterial replisome, revealed through single-molecule techniques, and to describe some aspects of the eukaryotic replisome under this framework. We primarily focus on Escherichia coli and Saccharomyces cerevisiae (budding yeast), since a significant amount of literature is available for these two model organisms. We end with a description of the methods of live-cell fluorescence microscopy for the characterization of replisome dynamics.
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11
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Replisome activity slowdown after exposure to ultraviolet light in Escherichia coli. Proc Natl Acad Sci U S A 2019; 116:11747-11753. [PMID: 31127046 DOI: 10.1073/pnas.1819297116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The replisome is a multiprotein machine that is responsible for replicating DNA. During active DNA synthesis, the replisome tightly associates with DNA. In contrast, after DNA damage, the replisome may disassemble, exposing DNA to breaks and threatening cell survival. Using live cell imaging, we studied the effect of UV light on the replisome of Escherichia coli Surprisingly, our results showed an increase in Pol III holoenzyme (Pol III HE) foci post-UV that do not colocalize with the DnaB helicase. Formation of these foci is independent of active replication forks and dependent on the presence of the χ subunit of the clamp loader, suggesting recruitment of Pol III HE at sites of DNA repair. Our results also showed a decrease of DnaB helicase foci per cell after UV, consistent with the disassembly of a fraction of the replisomes. By labeling newly synthesized DNA, we demonstrated that a drop in the rate of synthesis is not explained by replisome disassembly alone. Instead, we show that most replisomes continue synthesizing DNA at a slower rate after UV. We propose that the slowdown in replisome activity is a strategy to prevent clashes with engaged DNA repair proteins and preserve the integrity of the replication fork.
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12
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Kaguni JM. The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery. Antibiotics (Basel) 2018. [PMID: 29538288 PMCID: PMC5872134 DOI: 10.3390/antibiotics7010023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
DNA replication is an essential process. Although the fundamental strategies to duplicate chromosomes are similar in all free-living organisms, the enzymes of the three domains of life that perform similar functions in DNA replication differ in amino acid sequence and their three-dimensional structures. Moreover, the respective proteins generally utilize different enzymatic mechanisms. Hence, the replication proteins that are highly conserved among bacterial species are attractive targets to develop novel antibiotics as the compounds are unlikely to demonstrate off-target effects. For those proteins that differ among bacteria, compounds that are species-specific may be found. Escherichia coli has been developed as a model system to study DNA replication, serving as a benchmark for comparison. This review summarizes the functions of individual E. coli proteins, and the compounds that inhibit them.
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Affiliation(s)
- Jon M Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA.
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13
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Windgassen TA, Wessel SR, Bhattacharyya B, Keck JL. Mechanisms of bacterial DNA replication restart. Nucleic Acids Res 2018; 46:504-519. [PMID: 29202195 PMCID: PMC5778457 DOI: 10.1093/nar/gkx1203] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/21/2022] Open
Abstract
Multi-protein DNA replication complexes called replisomes perform the essential process of copying cellular genetic information prior to cell division. Under ideal conditions, replisomes dissociate only after the entire genome has been duplicated. However, DNA replication rarely occurs without interruptions that can dislodge replisomes from DNA. Such events produce incompletely replicated chromosomes that, if left unrepaired, prevent the segregation of full genomes to daughter cells. To mitigate this threat, cells have evolved 'DNA replication restart' pathways that have been best defined in bacteria. Replication restart requires recognition and remodeling of abandoned replication forks by DNA replication restart proteins followed by reloading of the replicative DNA helicase, which subsequently directs assembly of the remaining replisome subunits. This review summarizes our current understanding of the mechanisms underlying replication restart and the proteins that drive the process in Escherichia coli (PriA, PriB, PriC and DnaT).
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Affiliation(s)
- Tricia A Windgassen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Sarah R Wessel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
- Department of Biochemistry, Vanderbilt School of Medicine, Nashville, TN 37205, USA
| | - Basudeb Bhattacharyya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, La Crosse, WI 54601, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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14
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van Eijk E, Paschalis V, Green M, Friggen AH, Larson MA, Spriggs K, Briggs GS, Soultanas P, Smits WK. Primase is required for helicase activity and helicase alters the specificity of primase in the enteropathogen Clostridium difficile. Open Biol 2017; 6:rsob.160272. [PMID: 28003473 PMCID: PMC5204125 DOI: 10.1098/rsob.160272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 12/16/2022] Open
Abstract
DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by subtle mechanistic differences and limited understanding of DNA replication in pathogenic microorganisms. Clostridium difficile is the main cause of healthcare-associated diarrhoea and its DNA replication machinery is virtually uncharacterized. We identify and characterize the mechanistic details of the putative replicative helicase (CD3657), helicase-loader ATPase (CD3654) and primase (CD1454) of C. difficile, and reconstitute helicase and primase activities in vitro. We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. Furthermore, we find that helicase activity is dependent on the presence of primase in vitro. The inherent trinucleotide specificity of primase is determined by a single lysine residue and is similar to the primase of the extreme thermophile Aquifex aeolicus. However, the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, loader–helicase–primase interactions, which crucially mediate helicase loading and activation during DNA replication in all organisms, differ critically in C. difficile from that of the well-studied Gram-positive Bacillus subtilis model.
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Affiliation(s)
- Erika van Eijk
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Vasileios Paschalis
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Matthew Green
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Annemieke H Friggen
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marilynn A Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900, USA.,National Strategic Research Institute, Omaha, NE 68105, USA
| | | | - Geoffrey S Briggs
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Panos Soultanas
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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15
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Phenotypes of dnaXE145A Mutant Cells Indicate that the Escherichia coli Clamp Loader Has a Role in the Restart of Stalled Replication Forks. J Bacteriol 2017; 199:JB.00412-17. [PMID: 28947673 DOI: 10.1128/jb.00412-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/18/2017] [Indexed: 12/27/2022] Open
Abstract
The Escherichia colidnaXE145A mutation was discovered in connection with a screen for multicopy suppressors of the temperature-sensitive topoisomerase IV mutation parE10 The gene for the clamp loader subunits τ and γ, dnaX, but not the mutant dnaXE145A , was found to suppress parE10(Ts) when overexpressed. Purified mutant protein was found to be functional in vitro, and few phenotypes were found in vivo apart from problems with partitioning of DNA in rich medium. We show here that a large number of the replication forks that initiate at oriC never reach the terminus in dnaXE145A mutant cells. The SOS response was found to be induced, and a combination of the dnaXE145A mutation with recBC and recA mutations led to reduced viability. The mutant cells exhibited extensive chromosome fragmentation and degradation upon inactivation of recBC and recA, respectively. The results indicate that the dnaXE145A mutant cells suffer from broken replication forks and that these need to be repaired by homologous recombination. We suggest that the dnaX-encoded τ and γ subunits of the clamp loader, or the clamp loader complex itself, has a role in the restart of stalled replication forks without extensive homologous recombination.IMPORTANCE The E. coli clamp loader complex has a role in coordinating the activity of the replisome at the replication fork and loading β-clamps for lagging-strand synthesis. Replication forks frequently encounter obstacles, such as template lesions, secondary structures, and tightly bound protein complexes, which will lead to fork stalling. Some pathways of fork restart have been characterized, but much is still unknown about the actors and mechanisms involved. We have in this work characterized the dnaXE145A clamp loader mutant. We find that the naturally occurring obstacles encountered by a replication fork are not tackled in a proper way by the mutant clamp loader and suggest a role for the clamp loader in the restart of stalled replication forks.
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16
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Michel B, Sinha AK. The inactivation of rfaP, rarA or sspA gene improves the viability of the Escherichia coli DNA polymerase III holD mutant. Mol Microbiol 2017; 104:1008-1026. [PMID: 28342235 DOI: 10.1111/mmi.13677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 12/11/2022]
Abstract
The Escherichia coli holD mutant is poorly viable because the stability of holoenzyme polymerase III (Pol III HE) on DNA is compromised. Consequently, the SOS response is induced and the SOS polymerases DinB and Pol II further hinder replication. Mutations that restore the holD mutant viability belong to two classes, those that stabilize Pol III on DNA and those that prevent the deleterious effects of DinB over-production. We identified a dnaX mutation and the inactivation of rfaP and sspA genes as belonging to the first class of holD mutant suppressors. dnaX encodes a Pol III clamp loader subunit that interacts with HolD. rfaP encodes a lipopolysaccharide kinase that acts in outer membrane biogenesis. Its inactivation improves the holD mutant growth in part by affecting potassium import, previously proposed to stabilize Pol III HE on DNA by increasing electrostatic interactions. sspA encodes a global transcriptional regulator and growth of the holD mutant in its absence suggests that SspA controls genes that affect protein-DNA interactions. The inactivation of rarA belongs to the second class of suppressor mutations. rarA inactivation has a weak effect but is additive with other suppressor mutations. Our results suggest that RarA facilitates DinB binding to abandoned forks.
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Affiliation(s)
- Bénédicte Michel
- Genome Biology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Anurag Kumar Sinha
- Genome Biology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
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17
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Abstract
DNA replication in Escherichia coli initiates at oriC, the origin of replication and proceeds bidirectionally, resulting in two replication forks that travel in opposite directions from the origin. Here, we focus on events at the replication fork. The replication machinery (or replisome), first assembled on both forks at oriC, contains the DnaB helicase for strand separation, and the DNA polymerase III holoenzyme (Pol III HE) for DNA synthesis. DnaB interacts transiently with the DnaG primase for RNA priming on both strands. The Pol III HE is made up of three subassemblies: (i) the αɛθ core polymerase complex that is present in two (or three) copies to simultaneously copy both DNA strands, (ii) the β2 sliding clamp that interacts with the core polymerase to ensure its processivity, and (iii) the seven-subunit clamp loader complex that loads β2 onto primer-template junctions and interacts with the α polymerase subunit of the core and the DnaB helicase to organize the two (or three) core polymerases. Here, we review the structures of the enzymatic components of replisomes, and the protein-protein and protein-DNA interactions that ensure they remain intact while undergoing substantial dynamic changes as they function to copy both the leading and lagging strands simultaneously during coordinated replication.
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Affiliation(s)
- J S Lewis
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - S Jergic
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - N E Dixon
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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18
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Abstract
The cellular replicating machine, or "replisome," is composed of numerous different proteins. The core replication proteins in all cell types include a helicase, primase, DNA polymerases, sliding clamp, clamp loader, and single-strand binding (SSB) protein. The core eukaryotic replisome proteins evolved independently from those of bacteria and thus have distinct architectures and mechanisms of action. The core replisome proteins of the eukaryote include: an 11-subunit CMG helicase, DNA polymerase alpha-primase, leading strand DNA polymerase epsilon, lagging strand DNA polymerase delta, PCNA clamp, RFC clamp loader, and the RPA SSB protein. There are numerous other proteins that travel with eukaryotic replication forks, some of which are known to be involved in checkpoint regulation or nucleosome handling, but most have unknown functions and no bacterial analogue. Recent studies have revealed many structural and functional insights into replisome action. Also, the first structure of a replisome from any cell type has been elucidated for a eukaryote, consisting of 20 distinct proteins, with quite unexpected results. This review summarizes the current state of knowledge of the eukaryotic core replisome proteins, their structure, individual functions, and how they are organized at the replication fork as a machine.
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Affiliation(s)
- D Zhang
- The Rockefeller University, New York, NY, United States
| | - M O'Donnell
- The Rockefeller University, New York, NY, United States; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, United States.
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19
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Yuan Q, Dohrmann PR, Sutton MD, McHenry CS. DNA Polymerase III, but Not Polymerase IV, Must Be Bound to a τ-Containing DnaX Complex to Enable Exchange into Replication Forks. J Biol Chem 2016; 291:11727-35. [PMID: 27056333 DOI: 10.1074/jbc.m116.725358] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 11/06/2022] Open
Abstract
Examples of dynamic polymerase exchange have been previously characterized in model systems provided by coliphages T4 and T7. Using a dominant negative D403E polymerase (Pol) III α that can form initiation complexes and sequester primer termini but not elongate, we investigated the possibility of exchange at the Escherichia coli replication fork on a rolling circle template. Unlike other systems, addition of polymerase alone did not lead to exchange. Only when D403E Pol III was bound to a τ-containing DnaX complex did exchange occur. In contrast, addition of Pol IV led to rapid exchange in the absence of bound DnaX complex. Examination of Pol III* with varying composition of τ or the alternative shorter dnaX translation product γ showed that τ-, τ2-, or τ3-DnaX complexes supported equivalent levels of synthesis, identical Okazaki fragment size, and gaps between fragments, possessed the ability to challenge pre-established replication forks, and displayed equivalent susceptibility to challenge by exogenous D403E Pol III*. These findings reveal that redundant interactions at the replication fork must stabilize complexes containing only one τ. Previously, it was thought that at least two τs in the trimeric DnaX complex were required to couple the leading and lagging strand polymerases at the replication fork. Possible mechanisms of exchange are discussed.
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Affiliation(s)
- Quan Yuan
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303 and
| | - Paul R Dohrmann
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303 and
| | - Mark D Sutton
- the Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York 14214
| | - Charles S McHenry
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303 and
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20
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Dohrmann PR, Correa R, Frisch RL, Rosenberg SM, McHenry CS. The DNA polymerase III holoenzyme contains γ and is not a trimeric polymerase. Nucleic Acids Res 2016; 44:1285-97. [PMID: 26786318 PMCID: PMC4756838 DOI: 10.1093/nar/gkv1510] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
There is widespread agreement that the clamp loader of the Escherichia coli replicase has the composition DnaX3δδ’χψ. Two DnaX proteins exist in E. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds DNA polymerase III tightly; γ does not. There is a controversy as to whether or not DNA polymerase III holoenzyme (Pol III HE) contains γ. A three-τ form of Pol III HE would contain three Pol IIIs. Proponents of the three-τ hypothesis have claimed that γ found in Pol III HE might be a proteolysis product of τ. To resolve this controversy, we constructed a strain that expressed only τ from a mutated chromosomal dnaX. γ containing a C-terminal biotinylation tag (γ-Ctag) was provided in trans at physiological levels from a plasmid. A 2000-fold purification of Pol III* (all Pol III HE subunits except β) from this strain contained one molecule of γ-Ctag per Pol III* assembly, indicating that the dominant form of Pol III* in cells is Pol III2τ2 γδδ’χψ. Revealing a role for γ in cells, mutants that express only τ display sensitivity to ultraviolet light and reduction in DNA Pol IV-dependent mutagenesis associated with double-strand-break repair, and impaired maintenance of an F’ episome.
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Affiliation(s)
- Paul R Dohrmann
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | - Raul Correa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan L Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
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21
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Abstract
This review describes the components of the Escherichia coli replisome and the dynamic process in which they function and interact under normal conditions. It also briefly describes the behavior of the replisome during situations in which normal replication fork movement is disturbed, such as when the replication fork collides with sites of DNA damage. E. coli DNA Pol III was isolated first from a polA mutant E. coli strain that lacked the relatively abundant DNA Pol I activity. Further biochemical studies, and the use of double mutant strains, revealed Pol III to be the replicative DNA polymerase essential to cell viability. In a replisome, DnaG primase must interact with DnaB for activity, and this constraint ensures that new RNA primers localize to the replication fork. The leading strand polymerase continually synthesizes DNA in the direction of the replication fork, whereas the lagging-strand polymerase synthesizes short, discontinuous Okazaki fragments in the opposite direction. Discontinuous lagging-strand synthesis requires that the polymerase rapidly dissociate from each new completed Okazaki fragment in order to begin the extension of a new RNA primer. Lesion bypass can be thought of as a two-step reaction that starts with the incorporation of a nucleotide opposite the lesion, followed by the extension of the resulting distorted primer terminus. A remarkable property of E. coli, and many other eubacterial organisms, is the speed at which it propagates. Rapid cell division requires the presence of an extremely efficient replication machinery for the rapid and faithful duplication of the genome.
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22
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Lindow JC, Dohrmann PR, McHenry CS. DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection. J Biol Chem 2015; 290:16851-60. [PMID: 25987558 DOI: 10.1074/jbc.m115.661090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Indexed: 11/06/2022] Open
Abstract
Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first step of the replicase reaction: the ATP-dependent formation of an initiation complex between the Pol III HE and primed DNA. We exploited a genetic selection using a dominant negative variant of the polymerase catalytic subunit that can effectively compete with wild-type Pol III α and form initiation complexes, but cannot elongate. Suppression of the dominant negative phenotype was achieved by secondary mutations that were ineffective in initiation complex formation. The corresponding proteins were purified and characterized. One class of mutant mapped to the PHP domain of Pol III α, ablating interaction with the ϵ proofreading subunit and distorting the polymerase active site in the adjacent polymerase domain. Another class of mutation, found near the C terminus, interfered with τ binding. A third class mapped within the known β-binding domain, decreasing interaction with the β2 processivity factor. Surprisingly, mutations within the β binding domain also ablated interaction with τ, suggesting a larger τ binding site than previously recognized.
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Affiliation(s)
- Janet C Lindow
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Paul R Dohrmann
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Charles S McHenry
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
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23
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Georgescu R, Langston L, O'Donnell M. A proposal: Evolution of PCNA's role as a marker of newly replicated DNA. DNA Repair (Amst) 2015; 29:4-15. [PMID: 25704660 DOI: 10.1016/j.dnarep.2015.01.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 11/26/2022]
Abstract
Processivity clamps that hold DNA polymerases to DNA for processivity were the first proteins known to encircle the DNA duplex. At the time, polymerase processivity was thought to be the only function of ring shaped processivity clamps. But studies from many laboratories have identified numerous proteins that bind and function with sliding clamps. Among these processes are mismatch repair and nucleosome assembly. Interestingly, there exist polymerases that are highly processive and do not require clamps. Hence, DNA polymerase processivity does not intrinsically require that sliding clamps evolved for this purpose. We propose that polymerases evolved to require clamps as a way of ensuring that clamps are deposited on newly replicated DNA. These clamps are then used on the newly replicated daughter strands, for processes important to genomic integrity, such as mismatch repair and the assembly of nucleosomes to maintain epigenetic states of replicating cells during development.
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Affiliation(s)
- Roxana Georgescu
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States
| | - Lance Langston
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States
| | - Mike O'Donnell
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States.
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24
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Abstract
Reconstitution experiments using replication proteins from a number of different model organisms have firmly established that, in vitro, DNA replication is semi-discontinuous: continuous on the leading strand and discontinuous on the lagging strand. The mechanism by which DNA is replicated in vivo is less clear. In fact, there have been many observations of discontinuous replication in the absence of exogenous DNA-damaging agents. It has also been proposed that replication is discontinuous on the leading strand at least in part because of DNA lesion bypass. Several recent studies have revealed mechanistic details of pathways where replication of the leading strand introduces discontinuities. These mechanisms and their potential contributions to observations of discontinuous replication in vivo will be discussed.
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25
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Yeeles JTP, Marians KJ. Dynamics of leading-strand lesion skipping by the replisome. Mol Cell 2013; 52:855-65. [PMID: 24268579 DOI: 10.1016/j.molcel.2013.10.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/24/2013] [Accepted: 10/14/2013] [Indexed: 11/18/2022]
Abstract
The E. coli replisome stalls transiently when it encounters a lesion in the leading-strand template, skipping over the damage by reinitiating replication at a new primer synthesized downstream by the primase. We report here that template unwinding and lagging-strand synthesis continue downstream of the lesion at a reduced rate after replisome stalling, that one replisome is capable of skipping multiple lesions, and that the rate-limiting steps of replication restart involve the synthesis and activation of the new primer downstream. We also find little support for the concept that polymerase uncoupling, where extensive lagging-strand synthesis proceeds downstream in the absence of leading-strand synthesis, involves physical separation of the leading-strand polymerase from the replisome. Instead, our data indicate that extensive uncoupled replication likely results from a failure of the leading-strand polymerase still associated with the DNA helicase and the lagging-strand polymerase that are proceeding downstream to reinitiate synthesis.
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Affiliation(s)
- Joseph T P Yeeles
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Kenneth J Marians
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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26
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Ribeck N, Saleh OA. DNA unwinding by ring-shaped T4 helicase gp41 is hindered by tension on the occluded strand. PLoS One 2013; 8:e79237. [PMID: 24250825 PMCID: PMC3826741 DOI: 10.1371/journal.pone.0079237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/20/2013] [Indexed: 01/12/2023] Open
Abstract
The replicative helicase for bacteriophage T4 is gp41, which is a ring-shaped hexameric motor protein that achieves unwinding of dsDNA by translocating along one strand of ssDNA while forcing the opposite strand to the outside of the ring. While much study has been dedicated to the mechanism of binding and translocation along the ssDNA strand encircled by ring-shaped helicases, relatively little is known about the nature of the interaction with the opposite, ‘occluded’ strand. Here, we investigate the interplay between the bacteriophage T4 helicase gp41 and the ss/dsDNA fork by measuring, at the single-molecule level, DNA unwinding events on stretched DNA tethers in multiple geometries. We find that gp41 activity is significantly dependent on the geometry and tension of the occluded strand, suggesting an interaction between gp41 and the occluded strand that stimulates the helicase. However, the geometry dependence of gp41 activity is the opposite of that found previously for the E. coli hexameric helicase DnaB. Namely, tension applied between the occluded strand and dsDNA stem inhibits unwinding activity by gp41, while tension pulling apart the two ssDNA tails does not hinder its activity. This implies a distinct variation in helicase-occluded strand interactions among superfamily IV helicases, and we propose a speculative model for this interaction that is consistent with both the data presented here on gp41 and the data that had been previously reported for DnaB.
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Affiliation(s)
- Noah Ribeck
- Department of Physics, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Omar A. Saleh
- Department of Materials and Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail:
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27
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Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair. J Mol Biol 2013; 425:4802-19. [PMID: 24021816 DOI: 10.1016/j.jmb.2013.08.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/01/2013] [Accepted: 08/16/2013] [Indexed: 11/21/2022]
Abstract
Escherichia coli single-stranded DNA binding protein (SSB) plays essential roles in DNA replication, recombination and repair. SSB functions as a homotetramer with each subunit possessing a DNA binding domain (OB-fold) and an intrinsically disordered C-terminus, of which the last nine amino acids provide the site for interaction with at least a dozen other proteins that function in DNA metabolism. To examine how many C-termini are needed for SSB function, we engineered covalently linked forms of SSB that possess only one or two C-termini within a four-OB-fold "tetramer". Whereas E. coli expressing SSB with only two tails can survive, expression of a single-tailed SSB is dominant lethal. E. coli expressing only the two-tailed SSB recovers faster from exposure to DNA damaging agents but accumulates more mutations. A single-tailed SSB shows defects in coupled leading and lagging strand DNA replication and does not support replication restart in vitro. These deficiencies in vitro provide a plausible explanation for the lethality observed in vivo. These results indicate that a single SSB tetramer must interact simultaneously with multiple protein partners during some essential roles in genome maintenance.
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28
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Fate of the replisome following arrest by UV-induced DNA damage in Escherichia coli. Proc Natl Acad Sci U S A 2013; 110:11421-6. [PMID: 23801750 DOI: 10.1073/pnas.1300624110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate replication in the presence of DNA damage is essential to genome stability and viability in all cells. In Escherichia coli, DNA replication forks blocked by UV-induced damage undergo a partial resection and RecF-catalyzed regression before synthesis resumes. These processing events generate distinct structural intermediates on the DNA that can be visualized in vivo using 2D agarose gels. However, the fate and behavior of the stalled replisome remains a central uncharacterized question. Here, we use thermosensitive mutants to show that the replisome's polymerases uncouple and transiently dissociate from the DNA in vivo. Inactivation of α, β, or τ subunits within the replisome is sufficient to signal and induce the RecF-mediated processing events observed following UV damage. By contrast, the helicase-primase complex (DnaB and DnaG) remains critically associated with the fork, leading to a loss of fork integrity, degradation, and aberrant intermediates when disrupted. The results reveal a dynamic replisome, capable of partial disassembly to allow access to the obstruction, while retaining subunits that maintain fork licensing and direct reassembly to the appropriate location after processing has occurred.
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29
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Wallen JR, Majka J, Ellenberger T. Discrete interactions between bacteriophage T7 primase-helicase and DNA polymerase drive the formation of a priming complex containing two copies of DNA polymerase. Biochemistry 2013; 52:4026-36. [PMID: 23675753 DOI: 10.1021/bi400284j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replisomes are multiprotein complexes that coordinate the synthesis of leading and lagging DNA strands to increase the replication efficiency and reduce DNA strand breaks caused by stalling of replication forks. The bacteriophage T7 replisome is an economical machine that requires only four proteins for processive, coupled synthesis of two DNA strands. Here we characterize a complex between T7 primase-helicase and DNA polymerase on DNA that was trapped during the initiation of Okazaki fragment synthesis from an RNA primer. This priming complex consists of two DNA polymerases and a primase-helicase hexamer that assemble on the DNA template in an RNA-dependent manner. The zinc binding domain of the primase-helicase is essential for trapping the RNA primer in complex with the polymerase, and a unique loop located on the thumb of the polymerase also stabilizes this primer extension complex. Whereas one of the polymerases engages the primase-helicase and RNA primer on the lagging strand of a model replication fork, the second polymerase in the complex is also functional and can bind a primed template DNA. These results indicate that the T7 primase-helicase specifically engages two copies of DNA polymerase, which would allow the coordination of leading and lagging strand synthesis at a replication fork. Assembly of the T7 replisome is driven by intimate interactions between the DNA polymerase and multiple subunits of the primase-helicase hexamer.
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Affiliation(s)
- Jamie R Wallen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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30
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Structure of the PolIIIα-τc-DNA complex suggests an atomic model of the replisome. Structure 2013; 21:658-64. [PMID: 23478062 PMCID: PMC3652607 DOI: 10.1016/j.str.2013.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/22/2013] [Accepted: 02/01/2013] [Indexed: 01/07/2023]
Abstract
The C-terminal domain (CTD) of the τ subunit of the clamp loader (τc) binds to both the DnaB helicase and the DNA polymerase III α subunit (PolIIIα), and determines their relative positions and orientations on the leading and lagging strands. Here, we present a 3.2 Å resolution structure of Thermus aquaticus PolIIIα in complex with τc and a DNA substrate. The structure reveals that the CTD of τc interacts with the CTD of PolIIIα through its C-terminal helix and the adjacent loop. Additionally, in this complex PolIIIα displays an open conformation that includes the reorientations of the oligonucleotide-binding fold and the thumb domain, which may be an indirect result of crystal packing due to the presence of the τc. Nevertheless, the position of the τc on PolIIIα allows us to suggest an approximate model for how the PolIIIα is oriented and positioned on the DnaB helicase.
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31
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Hayes S, Erker C, Horbay MA, Marciniuk K, Wang W, Hayes C. Phage Lambda P protein: trans-activation, inhibition phenotypes and their suppression. Viruses 2013; 5:619-53. [PMID: 23389467 PMCID: PMC3640518 DOI: 10.3390/v5020619] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/21/2013] [Accepted: 01/29/2013] [Indexed: 11/16/2022] Open
Abstract
The initiation of bacteriophage λ replication depends upon interactions between the oriλ DNA site, phage proteins O and P, and E. coli host replication proteins. P exhibits a high affinity for DnaB, the major replicative helicase for unwinding double stranded DNA. The concept of P-lethality relates to the hypothesis that P can sequester DnaB and in turn prevent cellular replication initiation from oriC. Alternatively, it was suggested that P-lethality does not involve an interaction between P and DnaB, but is targeted to DnaA. P-lethality is assessed by examining host cells for transformation by ColE1-type plasmids that can express P, and the absence of transformants is attributed to a lethal effect of P expression. The plasmid we employed enabled conditional expression of P, where under permissive conditions, cells were efficiently transformed. We observed that ColE1 replication and plasmid establishment upon transformation is extremely sensitive to P, and distinguish this effect from P-lethality directed to cells. We show that alleles of dnaB protect the variant cells from P expression. P-dependent cellular filamentation arose in ΔrecA or lexA[Ind-] cells, defective for SOS induction. Replication propagation and restart could represent additional targets for P interference of E. coli replication, beyond the oriC-dependent initiation step.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada.
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32
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Abstract
Helicases are fundamental components of all replication complexes since unwinding of the double-stranded template to generate single-stranded DNA is essential to direct DNA synthesis by polymerases. However, helicases are also required in many other steps of DNA replication. Replicative helicases not only unwind the template DNA but also play key roles in regulating priming of DNA synthesis and coordination of leading and lagging strand DNA polymerases. Accessory helicases also aid replicative helicases in unwinding of the template strands in the presence of proteins bound to the DNA, minimising the risks posed by nucleoprotein complexes to continued fork movement. Helicases also play critical roles in Okazaki fragment processing in eukaryotes and may also be needed to minimise topological problems when replication forks converge. Thus fork movement, coordination of DNA synthesis, lagging strand maturation and termination of replication all depend on helicases. Moreover, if disaster strikes and a replication fork breaks down then reloading of the replication machinery is effected by helicases, at least in bacteria. This chapter describes how helicases function in these multiple steps at the fork and how DNA unwinding is coordinated with other catalytic processes to ensure efficient, high fidelity duplication of the genetic material in all organisms.
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Affiliation(s)
- Peter McGlynn
- Department of Biology, University of York, York, Yorkshire, UK,
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33
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Robinson A, Causer RJ, Dixon NE. Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target. Curr Drug Targets 2012; 13:352-72. [PMID: 22206257 PMCID: PMC3290774 DOI: 10.2174/138945012799424598] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 11/03/2011] [Accepted: 11/05/2011] [Indexed: 11/22/2022]
Abstract
New antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. Over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. We can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of new broad-spectrum antibacterials. DNA replication is a conserved and essential process, and the large number of proteins that interact to replicate DNA in bacteria are distinct from those in eukaryotes and archaea; yet none of the antibiotics in current clinical use acts directly on the replication machinery. Bacterial DNA synthesis thus appears to be an underexploited drug target. However, before this system can be targeted for drug design, it is important to understand which parts are conserved and which are not, as this will have implications for the spectrum of activity of any new inhibitors against bacterial species, as well as the potential for development of drug resistance. In this review we assess similarities and differences in replication components and mechanisms across the bacteria, highlight current progress towards the discovery of novel replication inhibitors, and suggest those aspects of the replication machinery that have the greatest potential as drug targets.
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Affiliation(s)
- Andrew Robinson
- School of Chemistry, University of Wollongong, NSW 2522, Australia
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34
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Fijalkowska IJ, Schaaper RM, Jonczyk P. DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair. FEMS Microbiol Rev 2012; 36:1105-21. [PMID: 22404288 DOI: 10.1111/j.1574-6976.2012.00338.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 02/29/2012] [Accepted: 03/01/2012] [Indexed: 12/21/2022] Open
Abstract
High accuracy (fidelity) of DNA replication is important for cells to preserve the genetic identity and to prevent the accumulation of deleterious mutations. The error rate during DNA replication is as low as 10(-9) to 10(-11) errors per base pair. How this low level is achieved is an issue of major interest. This review is concerned with the mechanisms underlying the fidelity of the chromosomal replication in the model system Escherichia coli by DNA polymerase III holoenzyme, with further emphasis on participation of the other, accessory DNA polymerases, of which E. coli contains four (Pols I, II, IV, and V). Detailed genetic analysis of mutation rates revealed that (1) Pol II has an important role as a back-up proofreader for Pol III, (2) Pols IV and V do not normally contribute significantly to replication fidelity, but can readily do so under conditions of elevated expression, (3) participation of Pols IV and V, in contrast to that of Pol II, is specific to the lagging strand, and (4) Pol I also makes a lagging-strand-specific fidelity contribution, limited, however, to the faithful filling of the Okazaki fragment gaps. The fidelity role of the Pol III τ subunit is also reviewed.
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Affiliation(s)
- Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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35
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Abstract
Bacterial replicases are complex, tripartite replicative machines. They contain a polymerase, polymerase III (Pol III), a β₂ processivity factor, and a DnaX complex ATPase that loads β₂ onto DNA and chaperones Pol III onto the newly loaded β₂. Bacterial replicases are highly processive, yet cycle rapidly during Okazaki fragment synthesis in a regulated way. Many bacteria encode both a full-length τ and a shorter γ form of DnaX by a variety of mechanisms. γ appears to be uniquely placed in a single position relative to two τ protomers in a pentameric ring. The polymerase catalytic subunit of Pol III, α, contains a PHP domain that not only binds to a prototypical ε Mg²⁺-dependent exonuclease, but also contains a second Zn²⁺-dependent proofreading exonuclease, at least in some bacteria. This review focuses on a critical evaluation of recent literature and concepts pertaining to the above issues and suggests specific areas that require further investigation.
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Affiliation(s)
- Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA.
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36
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Timinskas K, Venclovas Č. The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III τ subunit. FEBS J 2011; 278:3109-18. [DOI: 10.1111/j.1742-4658.2011.08236.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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37
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Downey CD, Crooke E, McHenry CS. Polymerase chaperoning and multiple ATPase sites enable the E. coli DNA polymerase III holoenzyme to rapidly form initiation complexes. J Mol Biol 2011; 412:340-53. [PMID: 21820444 DOI: 10.1016/j.jmb.2011.07.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 07/21/2011] [Accepted: 07/21/2011] [Indexed: 10/17/2022]
Abstract
Cellular replicases include three subassemblies: a DNA polymerase, a sliding clamp processivity factor, and a clamp loader complex. The Escherichia coli clamp loader is the DnaX complex (DnaX(3)δδ'χψ), where DnaX occurs either as τ or as the shorter γ that arises by translational frameshifting. Complexes composed of either form of DnaX are fully active clamp loaders, but τ confers important replicase functions including chaperoning the polymerase to the newly loaded clamp to form an initiation complex for processive replication. The kinetics of initiation complex formation were explored for DnaX complexes reconstituted with varying τ and γ stoichiometries, revealing that τ-mediated polymerase chaperoning accelerates initiation complex formation by 100-fold. Analyzing DnaX complexes containing one or more K51E variant DnaX subunits demonstrated that only one active ATP binding site is required to form initiation complexes, but the two additional sites increase the rate by ca 1000-fold. For τ-containing complexes, the ATP analogue ATPγS was found to support initiation complex formation at 1/1000th the rate with ATP. In contrast to previous models that proposed ATPγS drives hydrolysis-independent initiation complex formation by τ-containing complexes, the rate and stoichiometry of ATPγS hydrolysis coincide with those for initiation complex formation. These results show that although one ATPase site is sufficient for initiation complex formation, the combination of polymerase chaperoning and the binding and hydrolysis of three ATPs dramatically accelerates initiation complex formation to a rate constant (25-50 s(-1)) compatible with double-stranded DNA replication.
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Affiliation(s)
- Christopher D Downey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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38
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McHenry CS. Breaking the rules: bacteria that use several DNA polymerase IIIs. EMBO Rep 2011; 12:408-14. [PMID: 21475246 DOI: 10.1038/embor.2011.51] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/16/2011] [Indexed: 02/02/2023] Open
Abstract
Studies using Escherichia coli DNA polymerase (Pol) III as the prototype for bacterial DNA replication have suggested that--in contrast to eukaryotes--one replicase performs all of the main functions at the replication fork. However, recent studies have revealed that replication in other bacteria requires two forms of Pol III, one of which seems to extend RNA primers by only a few nucleotides before transferring the product to the other polymerase--an arrangement analogous to that in eukaryotes. Yet another group of bacteria encode a second Pol III (ImuC), which apparently replaces a Pol Y-type polymerase (Pol V) that is required for induced mutagenesis in E. coli. A complete understanding of complex bacterial replicases will allow the simultaneous biochemical screening of all their components and, thus, the identification of new antibacterial compounds.
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Affiliation(s)
- Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado, Chemistry 76, UCB 215, Boulder, Colorado 80309, USA.
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39
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dnaX36 Mutator of Escherichia coli: effects of the {tau} subunit of the DNA polymerase III holoenzyme on chromosomal DNA replication fidelity. J Bacteriol 2010; 193:296-300. [PMID: 21036999 DOI: 10.1128/jb.01191-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli dnaX36 mutant displays a mutator effect, reflecting a fidelity function of the dnaX-encoded τ subunit of the DNA polymerase III (Pol III) holoenzyme. We have shown that this fidelity function (i) applies to both leading- and lagging-strand synthesis, (ii) is independent of Pol IV, and (iii) is limited by Pol II.
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40
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Essential biological processes of an emerging pathogen: DNA replication, transcription, and cell division in Acinetobacter spp. Microbiol Mol Biol Rev 2010; 74:273-97. [PMID: 20508250 DOI: 10.1128/mmbr.00048-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Within the last 15 years, members of the bacterial genus Acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. The driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. There is an urgent need for new antibacterial compounds to combat the threat imposed by Acinetobacter spp. and other intractable bacterial pathogens. The essential processes of chromosomal DNA replication, transcription, and cell division are attractive targets for the rational design of antimicrobial drugs. The goal of this review is to examine the wealth of genome sequence and gene knockout data now available for Acinetobacter spp., highlighting those aspects of essential systems that are most suitable as drug targets. Acinetobacter spp. show several key differences from other pathogenic gammaproteobacteria, particularly in global stress response pathways. The involvement of these pathways in short- and long-term antibiotic survival suggests that Acinetobacter spp. cope with antibiotic-induced stress differently from other microorganisms.
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41
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Park AY, Jergic S, Politis A, Ruotolo BT, Hirshberg D, Jessop LL, Beck JL, Barsky D, O'Donnell M, Dixon NE, Robinson CV. A single subunit directs the assembly of the Escherichia coli DNA sliding clamp loader. Structure 2010; 18:285-92. [PMID: 20223211 DOI: 10.1016/j.str.2010.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 01/19/2010] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
Abstract
Multi-protein clamp loader complexes are required to load sliding clamps onto DNA. In Escherichia coli the clamp loader contains three DnaX (tau/gamma) proteins, delta, and delta', which together form an asymmetric pentameric ring that also interacts with psichi. Here we used mass spectrometry to examine the assembly and dynamics of the clamp loader complex. We find that gamma exists exclusively as a stable homotetramer, while tau is in a monomer-dimer-trimer-tetramer equilibrium. delta' plays a direct role in the assembly as a tau/gamma oligomer breaker, thereby facilitating incorporation of lower oligomers. With delta', both delta and psichi stabilize the trimeric form of DnaX, thus completing the assembly. When tau and gamma are present simultaneously, mimicking the situation in vivo, subunit exchange between tau and gamma tetramers occurs rapidly to form heterocomplexes but is retarded when deltadelta' is present. The implications for intracellular assembly of the DNA polymerase III holoenzyme are discussed.
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Affiliation(s)
- Ah Young Park
- Department of Chemistry, University of Oxford, Oxford, UK
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42
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Downey CD, McHenry CS. Chaperoning of a replicative polymerase onto a newly assembled DNA-bound sliding clamp by the clamp loader. Mol Cell 2010; 37:481-91. [PMID: 20188667 DOI: 10.1016/j.molcel.2010.01.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/03/2009] [Accepted: 11/12/2009] [Indexed: 11/29/2022]
Abstract
Cellular replicases contain multiprotein ATPases that load sliding clamp processivity factors onto DNA. We reveal an additional role for the DnaX clamp loader: chaperoning of the replicative polymerase onto a clamp newly bound to DNA. We show that chaperoning confers distinct advantages, including marked acceleration of initiation complex formation. We reveal a requirement for the tau form of DnaX complex to relieve inhibition by single-stranded DNA binding protein during initiation complex formation. We propose that, after loading beta(2), DnaX complex preserves an SSB-free segment of DNA immediately downstream of the primer terminus and chaperones Pol III into that position, preventing competition by SSB. The C-terminal tail of SSB stimulates reactions catalyzed by tau-containing DnaX complexes through a contact distinct from the contact involving the chi subunit. Chaperoning of Pol III by the DnaX complex provides a molecular explanation for how initiation complexes form when supported by the nonhydrolyzed analog ATPgammaS.
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Affiliation(s)
- Christopher D Downey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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43
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Langston LD, Indiani C, O'Donnell M. Whither the replisome: emerging perspectives on the dynamic nature of the DNA replication machinery. Cell Cycle 2009; 8:2686-91. [PMID: 19652539 DOI: 10.4161/cc.8.17.9390] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Replisomes were originally thought to be multi-protein machines with a stabile and defined structure during replication. Discovery that replisomes repeatedly discard sliding clamps and assemble a new clamp to start each Okazaki fragment provided the first hint that the replisome structure changes during replication. Recent studies reveal that the replisome is more dynamic than ever thought possible. Replisomes can utilize many different polymerases; the helicase is regulated to travel at widely different speeds; leading and lagging strands need not always act in a coupled fashion with DNA loops; and the replication fork does not always exhibit semi-discontinuous replication. We review some of these findings here and discuss their implications for cell physiology as well as enzyme mechanism.
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44
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Park MS, O'Donnell M. The clamp loader assembles the beta clamp onto either a 3' or 5' primer terminus: the underlying basis favoring 3' loading. J Biol Chem 2009; 284:31473-83. [PMID: 19759020 DOI: 10.1074/jbc.m109.050310] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clamp loaders assemble sliding clamps onto 3' primed sites for DNA polymerases. Clamp loaders are thought to be specific for a 3' primed site, and unable to bind a 5' site. We demonstrate here that the Escherichia coli gamma complex clamp loader can load the beta clamp onto a 5' primed site, although with at least 20-fold reduced efficiency relative to loading at a 3' primed site. Preferential clamp loading at a 3' site does not appear to be due to DNA binding, as the clamp loader forms an avid complex with beta at a 5' site. Preferential loading at a 3' versus a 5' site occurs at the ATP hydrolysis step, needed to close the ring around DNA. We also address DNA structural features that are recognized for preferential loading at a 3' site. Although the single-stranded template strand extends in opposite directions from 3' and 5' primed sites, thus making it a favorite candidate for distinguishing between 3' and 5' sites, the single-strand polarity at a primed template junction does not determine 3' site selection for clamp loading. Instead, we find that clamp loader recognition of a 3' site lies in the duplex portion of the primed site, not the single-strand portion. We present evidence that the beta clamp facilitates its own loading specificity for a 3' primed site. Implications to eukaryotic clamp loader complexes are proposed.
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Affiliation(s)
- Mee Sook Park
- Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065, USA
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45
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Yuan Q, McHenry CS. Strand displacement by DNA polymerase III occurs through a tau-psi-chi link to single-stranded DNA-binding protein coating the lagging strand template. J Biol Chem 2009; 284:31672-9. [PMID: 19749191 DOI: 10.1074/jbc.m109.050740] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of gamma-complex to support the reaction in the absence of tau. However, if gamma-complex is present to load beta(2), a truncated tau protein containing only domains III-V will suffice. This truncated protein is sufficient to bind both the alpha subunit of DNA polymerase (Pol) III and chipsi. This is reminiscent of the minimal requirements for Pol III to replicate short single-stranded DNA-binding protein (SSB)-coated templates where tau is only required to serve as a scaffold to hold Pol III and chi in the same complex (Glover, B., and McHenry, C. (1998) J. Biol. Chem. 273, 23476-23484). We propose a model in which strand displacement by DNA polymerase III holoenzyme depends upon a Pol III-tau-psi-chi-SSB binding network, where SSB is bound to the displaced strand, stabilizing the Pol III-template interaction. The same interaction network is probably important for stabilizing the leading strand polymerase interactions with authentic replication forks. The specificity constant (k(cat)/K(m)) for the strand displacement reaction is approximately 300-fold less favorable than reactions on single-stranded templates and proceeds with a slower rate (150 nucleotides/s) and only moderate processivity (approximately 300 nucleotides). PriA, the initiator of replication restart on collapsed or misassembled replication forks, blocks the strand displacement reaction, even if added to an ongoing reaction.
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Affiliation(s)
- Quan Yuan
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
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46
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Abstract
Replisomes are the protein assemblies that replicate DNA. They function as molecular motors to catalyze template-mediated polymerization of nucleotides, unwinding of DNA, the synthesis of RNA primers, and the assembly of proteins on DNA. The replisome of bacteriophage T7 contains a minimum of proteins, thus facilitating its study. This review describes the molecular motors and coordination of their activities, with emphasis on the T7 replisome. Nucleotide selection, movement of the polymerase, binding of the processivity factor, unwinding of DNA, and RNA primer synthesis all require conformational changes and protein contacts. Lagging-strand synthesis is mediated via a replication loop whose formation and resolution is dictated by switches to yield Okazaki fragments of discrete size. Both strands are synthesized at identical rates, controlled by a molecular brake that halts leading-strand synthesis during primer synthesis. The helicase serves as a reservoir for polymerases that can initiate DNA synthesis at the replication fork. We comment on the differences in other systems where applicable.
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Affiliation(s)
- Samir M Hamdan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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47
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Chintakayala K, Machón C, Haroniti A, Larson MA, Hinrichs SH, Griep MA, Soultanas P. Allosteric regulation of the primase (DnaG) activity by the clamp-loader (tau) in vitro. Mol Microbiol 2009; 72:537-49. [PMID: 19415803 DOI: 10.1111/j.1365-2958.2009.06668.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
During DNA replication the helicase (DnaB) recruits the primase (DnaG) in the replisome to initiate the polymerization of new DNA strands. DnaB is attached to the tau subunit of the clamp-loader that loads the beta clamp and interconnects the core polymerases on the leading and lagging strands. The tau-DnaB-DnaG ternary complex is at the heart of the replisome and its function is likely to be modulated by a complex network of allosteric interactions. Using a stable ternary complex comprising the primase and helicase from Geobacillus stearothermophilus and the tau subunit of the clamp-loader from Bacillus subtilis we show that changes in the DnaB-tau interaction can stimulate allosterically primer synthesis by DnaG in vitro. The A550V tau mutant stimulates the primase activity more efficiently than the native protein. Truncation of the last 18 C-terminal residues of tau elicits a DnaG-stimulatory effect in vitro that appears to be suppressed in the native tau protein. Thus changes in the tau-DnaB interaction allosterically affect primer synthesis. Although these C-terminal residues of tau are not involved directly in the interaction with DnaB, they may act as a functional gateway for regulation of primer synthesis by tau-interacting components of the replisome through the tau-DnaB-DnaG pathway.
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Affiliation(s)
- Kiran Chintakayala
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham, UK
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48
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Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase. Proc Natl Acad Sci U S A 2009; 106:6031-8. [PMID: 19279203 DOI: 10.1073/pnas.0901403106] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All cells contain specialized translesion DNA polymerases that replicate past sites of DNA damage. We find that Escherichia coli translesion DNA polymerase II (Pol II) and polymerase IV (Pol IV) function with DnaB helicase and regulate its rate of unwinding, slowing it to as little as 1 bp/s. Furthermore, Pol II and Pol IV freely exchange with the polymerase III (Pol III) replicase on the beta-clamp and function with DnaB helicase to form alternative replisomes, even before Pol III stalls at a lesion. DNA damage-induced levels of Pol II and Pol IV dominate the clamp, slowing the helicase and stably maintaining the architecture of the replication machinery while keeping the fork moving. We propose that these dynamic actions provide additional time for normal excision repair of lesions before the replication fork reaches them and also enable the appropriate translesion polymerase to sample each lesion as it is encountered.
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49
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An essential DnaB helicase of Bacillus anthracis: identification, characterization, and mechanism of action. J Bacteriol 2008; 191:249-60. [PMID: 18931108 DOI: 10.1128/jb.01259-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have described a novel essential replicative DNA helicase from Bacillus anthracis, the identification of its gene, and the elucidation of its enzymatic characteristics. Anthrax DnaB helicase (DnaB(BA)) is a 453-amino-acid, 50-kDa polypeptide with ATPase and DNA helicase activities. DnaB(BA) displayed distinct enzymatic and kinetic properties. DnaB(BA) has low single-stranded DNA (ssDNA)-dependent ATPase activity but possesses a strong 5'-->3' DNA helicase activity. The stimulation of ATPase activity appeared to be a function of the length of the ssDNA template rather than of ssDNA binding alone. The highest specific activity was observed with M13mp19 ssDNA. The results presented here indicated that the ATPase activity of DnaB(BA) was coupled to its migration on an ssDNA template rather than to DNA binding alone. It did not require nucleotide to bind ssDNA. DnaB(BA) demonstrated a strong DNA helicase activity that required ATP or dATP. Therefore, DnaB(BA) has an attenuated ATPase activity and a highly active DNA helicase activity. Based on the ratio of DNA helicase and ATPase activities, DnaB(BA) is highly efficient in DNA unwinding and its coupling to ATP consumption.
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50
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Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant. J Bacteriol 2007; 190:1730-42. [PMID: 18156258 DOI: 10.1128/jb.01463-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The dnaX36(TS) mutant of Escherichia coli confers a distinct mutator phenotype characterized by enhancement of transversion base substitutions and certain (-1) frameshift mutations. Here, we have further investigated the possible mechanism(s) underlying this mutator effect, focusing in particular on the role of the various E. coli DNA polymerases. The dnaX gene encodes the tau subunit of DNA polymerase III (Pol III) holoenzyme, the enzyme responsible for replication of the bacterial chromosome. The dnaX36 defect resides in the C-terminal domain V of tau, essential for interaction of tau with the alpha (polymerase) subunit, suggesting that the mutator phenotype is caused by an impaired or altered alpha-tau interaction. We previously proposed that the mutator activity results from aberrant processing of terminal mismatches created by Pol III insertion errors. The present results, including lack of interaction of dnaX36 with mutM, mutY, and recA defects, support our assumption that dnaX36-mediated mutations originate as errors of replication rather than DNA damage-related events. Second, an important role is described for DNA Pol II and Pol IV in preventing and producing, respectively, the mutations. In the system used, a high fraction of the mutations is dependent on the action of Pol IV in a (dinB) gene dosage-dependent manner. However, an even larger but opposing role is deduced for Pol II, revealing Pol II to be a major editor of Pol III mediated replication errors. Overall, the results provide insight into the interplay of the various DNA polymerases, and of tau subunit, in securing a high fidelity of replication.
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