1
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Harami GM, Pálinkás J, Seol Y, Kovács ZJ, Gyimesi M, Harami-Papp H, Neuman KC, Kovács M. The toposiomerase IIIalpha-RMI1-RMI2 complex orients human Bloom's syndrome helicase for efficient disruption of D-loops. Nat Commun 2022; 13:654. [PMID: 35115525 PMCID: PMC8813930 DOI: 10.1038/s41467-022-28208-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 01/12/2022] [Indexed: 01/05/2023] Open
Abstract
Homologous recombination (HR) is a ubiquitous and efficient process that serves the repair of severe forms of DNA damage and the generation of genetic diversity during meiosis. HR can proceed via multiple pathways with different outcomes that may aid or impair genome stability and faithful inheritance, underscoring the importance of HR quality control. Human Bloom's syndrome (BLM, RecQ family) helicase plays central roles in HR pathway selection and quality control via unexplored molecular mechanisms. Here we show that BLM's multi-domain structural architecture supports a balance between stabilization and disruption of displacement loops (D-loops), early HR intermediates that are key targets for HR regulation. We find that this balance is markedly shifted toward efficient D-loop disruption by the presence of BLM's interaction partners Topoisomerase IIIα-RMI1-RMI2, which have been shown to be involved in multiple steps of HR-based DNA repair. Our results point to a mechanism whereby BLM can differentially process D-loops and support HR control depending on cellular regulatory mechanisms.
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Affiliation(s)
- Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary. .,Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA.
| | - János Pálinkás
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Zoltán J Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary
| | - Máté Gyimesi
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary.,MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary
| | - Hajnalka Harami-Papp
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary.,Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary. .,MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary.
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2
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Measurement of Nucleotide Hydrolysis Using Fluorescent Biosensors for Phosphate. Methods Mol Biol 2021; 2263:289-318. [PMID: 33877604 DOI: 10.1007/978-1-0716-1197-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Assays for the detection of inorganic phosphate (Pi) are widely used to measure the activity of nucleotide hydrolyzing enzymes, such as ATPases and GTPases. The fluorescent biosensors for Pi, described here, are based on fluorescently labeled versions of E. coli phosphate-binding protein (PBP), which translates Pi binding into a large change in fluorescence intensity. In comparison with other Pi-detection systems, these biosensors are characterized by a high sensitivity (sub-micromolar Pi concentrations) and high time resolution (tens of milliseconds), and they are therefore particularly well suited for measurements of phosphate ester hydrolysis in real time. In this chapter, it is described how the Pi biosensors can be used to measure kinetics of ATPase and GTPase reactions, both under steady state and pre-steady state conditions. An example protocol is given for determining steady state kinetic parameters, Km and kcat, of the ATP-dependent chromatin remodeler Chd1, in a plate reader format. In addition, the measurement of Pi release kinetics under pre-steady state conditions is described, including a detailed experimental procedure for a single turnover measurement of ATP hydrolysis by the ABC-type ATPase SufBC using rapid mixing.
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3
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Szeltner Z, Póti Á, Harami GM, Kovács M, Szüts D. Evaluation and modulation of DNA lesion bypass in an SV40 large T antigen-based in vitro replication system. FEBS Open Bio 2021; 11:1054-1075. [PMID: 33512058 PMCID: PMC8016126 DOI: 10.1002/2211-5463.13099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 11/09/2022] Open
Abstract
DNA damage removal by nucleotide excision repair (NER) and replicative bypass via translesion synthesis (TLS) and template switch (TSw) are important in ensuring genome stability. In this study, we tested the applicability of an SV40 large T antigen‐based replication system for the simultaneous examination of these damage tolerance processes. Using both Sanger and next‐generation sequencing combined with lesion‐specific qPCR and replication efficiency studies, we demonstrate that this system works well for studying NER and TLS, especially its one‐polymerase branch, while it is less suited to investigations of homology‐related repair processes, such as TSw. Cis‐syn cyclobutane pyrimidine dimer photoproducts were replicated with equal efficiency to lesion‐free plasmids in vitro, and the majority of TLS on this lesion could be inhibited by a peptide (PIR) specific for the polη‐PCNA interaction interface. TLS on 6–4 pyrimidine–pyrimidone photoproduct proved to be inefficient and was slightly facilitated by PIR as well as by a recombinant ubiquitin‐binding zinc finger domain of polη in HeLa extract, possibly by promoting polymerase exchange. Supplementation of the extract with recombinant PCNA variants indicated the dependence of TLS on PCNA ubiquitylation. In contrast to active TLS and NER, we found no evidence of successful TSw in cellular extracts. The established methods can promote in vitro investigations of replicative DNA damage bypass.
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Affiliation(s)
- Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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4
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Jing C, Yu F, Zhang N, Liu Y, Wang H. Quantitative assessments of adenosine triphosphatase hydrolytic activity by ultrafiltration-coupled ion-pair reversed-phase high-performance liquid chromatography. J Sep Sci 2020; 43:3840-3846. [PMID: 32776712 DOI: 10.1002/jssc.202000561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/05/2020] [Accepted: 08/04/2020] [Indexed: 01/01/2023]
Abstract
Adenosine triphosphate is a universal energy currency that can directly provide energy required for a multitude of biochemical reactions and biophysical actions through adenosine triphosphatase catalyzed hydrolysis. Adenosine triphosphatase activity is thus one important feature for the characterization of protein function and cell activity. Herein, we optimized ion-pair reversed-phase high-performance liquid chromatography technique for highly efficient separation of adenosine triphosphate, adenosine diphosphate, and adenosine monophosphate, and the method demonstrated good linearity. Moreover, by coupling a protein-removable ultrafiltration, we developed a sensitive and robust approach for quantification of adenosine triphosphatase hydrolytic activity. By this assay, we demonstrated that RecA filaments-catalyzed adenosine triphosphate hydrolysis approached a second-order reaction, and its rate constant was estimated as 0.057 mM-1 min-1 . In addition, we explored the effects of DNA length on this reaction and revealed that the increase of the length of single-stranded DNA can promote the adenosine triphosphatase hydrolytic activity of RecA filaments. All these results confirm the feasibility of this new method in quantification of adenosine triphosphatase hydrolytic activity assays. Compared with previous complicated enzyme-coupled or homogeneous colorimetric measurements, the developed approach with high resolution separation allows a simple reaction system for adenosine triphosphatase assay and a sensitive detection free of interference from background noise.
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Affiliation(s)
- Changheng Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Fangzhi Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Ning Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P. R. China
| | - Yan Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
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5
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Chakrabarti S, Jarzynski C, Thirumalai D. Processivity, Velocity, and Universal Characteristics of Nucleic Acid Unwinding by Helicases. Biophys J 2019; 117:867-879. [PMID: 31400912 PMCID: PMC6731385 DOI: 10.1016/j.bpj.2019.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/20/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022] Open
Abstract
Helicases are components of the cellular replisome that are essential for unwinding double-strand nucleic acids during the process of replication. Intriguingly, most helicases are inefficient and require either oligomerization or assistance from other partner proteins to increase the processivity of unwinding in the presence of the replication fork, which acts as a barrier to progress. Single-molecule force spectroscopy has emerged as a promising experimental technique to probe how relieving this barrier on the helicase can allow for increased efficiency of unwinding. However, there exists no comprehensive theoretical framework to provide unique interpretations of the underlying helicase kinetics from the force spectroscopy data. This remains a major confounding issue in the field. Here, we develop a mathematical framework and derive analytic expressions for the velocity and run length of a general model of finitely processive helicases, the two most commonly measured experimental quantities. We show that in contrast to the unwinding velocity, the processivity exhibits a universal increase in response to external force, irrespective of the underlying architecture and unwinding kinetics of the helicase. Our work provides the first, to our knowledge, explanation to a wide array of experiments and suggests that helicases may have evolved to maximize processivity rather than speed. To demonstrate the use of our theory on experimental data, we analyze velocity and processivity data on the T7 helicase and provide unique inferences on the kinetics of the helicase. Our results show that T7 is a weakly active helicase that destabilizes the fork ahead by less than 1 kBT and back steps very frequently while unwinding DNA. Our work generates fundamental insights into the force response of helicases and provides a widely applicable method for inferring the underlying helicase kinetics from force spectroscopy data.
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Affiliation(s)
- Shaon Chakrabarti
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.
| | - Christopher Jarzynski
- Department of Chemistry and Biochemistry, Institute for Physical Sciences and Technology, Department of Physics, University of Maryland, College Park, Maryland
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
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6
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Seol Y, Harami GM, Kovács M, Neuman KC. Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase. eLife 2019; 8:e45909. [PMID: 31464683 PMCID: PMC6773442 DOI: 10.7554/elife.45909] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
RecQ helicases promote genomic stability through their unique ability to suppress illegitimate recombination and resolve recombination intermediates. These DNA structure-specific activities of RecQ helicases are mediated by the helicase-and-RNAseD like C-terminal (HRDC) domain, via unknown mechanisms. Here, employing single-molecule magnetic tweezers and rapid kinetic approaches we establish that the HRDC domain stabilizes intrinsic, sequence-dependent, pauses of the core helicase (lacking the HRDC) in a DNA geometry-dependent manner. We elucidate the core unwinding mechanism in which the unwinding rate depends on the stability of the duplex DNA leading to transient sequence-dependent pauses. We further demonstrate a non-linear amplification of these transient pauses by the controlled binding of the HRDC domain. The resulting DNA sequence- and geometry-dependent pausing may underlie a homology sensing mechanism that allows rapid disruption of unstable (illegitimate) and stabilization of stable (legitimate) DNA strand invasions, which suggests an intrinsic mechanism of recombination quality control by RecQ helicases.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule BiophysicsNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaUnited States
| | - Gábor M Harami
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research GroupEötvös Loránd UniversityBudapestHungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research GroupEötvös Loránd UniversityBudapestHungary
- Department of Biochemistry, MTA-ELTE Motor Pharmacology Research GroupEötvös Loránd UniversityBudapestHungary
| | - Keir C Neuman
- Laboratory of Single Molecule BiophysicsNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaUnited States
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7
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Bagchi D, Manosas M, Zhang W, Manthei KA, Hodeib S, Ducos B, Keck JL, Croquette V. Single molecule kinetics uncover roles for E. coli RecQ DNA helicase domains and interaction with SSB. Nucleic Acids Res 2019; 46:8500-8515. [PMID: 30053104 PMCID: PMC6144805 DOI: 10.1093/nar/gky647] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/15/2018] [Indexed: 12/16/2022] Open
Abstract
Most RecQ DNA helicases share a conserved domain arrangement that mediates their activities in genomic stability. This arrangement comprises a helicase motor domain, a RecQ C-terminal (RecQ-C) region including a winged-helix (WH) domain, and a ‘Helicase and RNase D C-terminal’ (HRDC) domain. Single-molecule real-time translocation and DNA unwinding by full-length Escherichia coli RecQ and variants lacking either the HRDC or both the WH and HRDC domains was analyzed. RecQ operated under two interconvertible kinetic modes, ‘slow’ and ‘normal’, as it unwound duplex DNA and translocated on single-stranded (ss) DNA. Consistent with a crystal structure of bacterial RecQ bound to ssDNA by base stacking, abasic sites blocked RecQ unwinding. Removal of the HRDC domain eliminates the slow mode while preserving the normal mode of activity. Unexpectedly, a RecQ variant lacking both the WH and HRDC domains retains weak helicase activity. The inclusion of E. coli ssDNA-binding protein (SSB) induces a third ‘fast’ unwinding mode four times faster than the normal RecQ mode and enhances the overall helicase activity (affinity, rate, and processivity). SSB stimulation was, furthermore, observed in the RecQ deletion variants, including the variant missing the WH domain. Our results support a model in which RecQ and SSB have multiple interacting modes.
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Affiliation(s)
- Debjani Bagchi
- Physics Department, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390002, India
| | - Maria Manosas
- Departament de Física de la Materia Condensada, Universitat de Barcelona, Barcelona 08028, Spain.,CIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain
| | - Weiting Zhang
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Kelly A Manthei
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | - Samar Hodeib
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Bertrand Ducos
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | - Vincent Croquette
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
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8
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Kasaciunaite K, Fettes F, Levikova M, Daldrop P, Anand R, Cejka P, Seidel R. Competing interaction partners modulate the activity of Sgs1 helicase during DNA end resection. EMBO J 2019; 38:e101516. [PMID: 31268598 PMCID: PMC6601037 DOI: 10.15252/embj.2019101516] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/24/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
DNA double-strand break repair by homologous recombination employs long-range resection of the 5' DNA ends at the break points. In Saccharomyces cerevisiae, this process can be performed by the RecQ helicase Sgs1 and the helicase-nuclease Dna2. Though functional interplay between them has been shown, it remains unclear whether and how these proteins cooperate on the molecular level. Here, we resolved the dynamics of DNA unwinding by Sgs1 at the single-molecule level and investigated Sgs1 regulation by Dna2, the single-stranded DNA-binding protein RPA, and the Top3-Rmi1 complex. We found that Dna2 modulates the velocity of Sgs1, indicating that during end resection both proteins form a functional complex and couple their activities. Sgs1 drives DNA unwinding and feeds single-stranded DNA to Dna2 for degradation. RPA was found to regulate the processivity and the affinity of Sgs1 to the DNA fork, while Top3-Rmi1 modulated the velocity of Sgs1. We hypothesize that the differential regulation of Sgs1 activity by its protein partners is important to support diverse cellular functions of Sgs1 during the maintenance of genome stability.
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Affiliation(s)
- Kristina Kasaciunaite
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Fergus Fettes
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Maryna Levikova
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Peter Daldrop
- Institute for Molecular Cell Biology, University of Münster, Münster, Germany
| | - Roopesh Anand
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
- Institute for Molecular Cell Biology, University of Münster, Münster, Germany
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9
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Mills M, Harami GM, Seol Y, Gyimesi M, Martina M, Kovács ZJ, Kovács M, Neuman KC. RecQ helicase triggers a binding mode change in the SSB-DNA complex to efficiently initiate DNA unwinding. Nucleic Acids Res 2017; 45:11878-11890. [PMID: 29059328 PMCID: PMC5714189 DOI: 10.1093/nar/gkx939] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/29/2017] [Accepted: 10/09/2017] [Indexed: 11/12/2022] Open
Abstract
The single-stranded DNA binding protein (SSB) of Escherichia coli plays essential roles in maintaining genome integrity by sequestering ssDNA and mediating DNA processing pathways through interactions with DNA-processing enzymes. Despite its DNA-sequestering properties, SSB stimulates the DNA processing activities of some of its binding partners. One example is the genome maintenance protein RecQ helicase. Here, we determine the mechanistic details of the RecQ-SSB interaction using single-molecule magnetic tweezers and rapid kinetic experiments. Our results reveal that the SSB-RecQ interaction changes the binding mode of SSB, thereby allowing RecQ to gain access to ssDNA and facilitating DNA unwinding. Conversely, the interaction of RecQ with the SSB C-terminal tail increases the on-rate of RecQ-DNA binding and has a modest stimulatory effect on the unwinding rate of RecQ. We propose that this bidirectional communication promotes efficient DNA processing and explains how SSB stimulates rather than inhibits RecQ activity.
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Affiliation(s)
- Maria Mills
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gábor M. Harami
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Máté Gyimesi
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Máté Martina
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Zoltán J. Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Shuttling along DNA and directed processing of D-loops by RecQ helicase support quality control of homologous recombination. Proc Natl Acad Sci U S A 2017; 114:E466-E475. [PMID: 28069956 DOI: 10.1073/pnas.1615439114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells must continuously repair inevitable DNA damage while avoiding the deleterious consequences of imprecise repair. Distinction between legitimate and illegitimate repair processes is thought to be achieved in part through differential recognition and processing of specific noncanonical DNA structures, although the mechanistic basis of discrimination remains poorly defined. Here, we show that Escherichia coli RecQ, a central DNA recombination and repair enzyme, exhibits differential processing of DNA substrates based on their geometry and structure. Through single-molecule and ensemble biophysical experiments, we elucidate how the conserved domain architecture of RecQ supports geometry-dependent shuttling and directed processing of recombination-intermediate [displacement loop (D-loop)] substrates. Our study shows that these activities together suppress illegitimate recombination in vivo, whereas unregulated duplex unwinding is detrimental for recombination precision. Based on these results, we propose a mechanism through which RecQ helicases achieve recombination precision and efficiency.
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11
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Pavankumar TL, Exell JC, Kowalczykowski SC. Direct Fluorescent Imaging of Translocation and Unwinding by Individual DNA Helicases. Methods Enzymol 2016; 581:1-32. [PMID: 27793277 DOI: 10.1016/bs.mie.2016.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The unique translocation and DNA unwinding properties of DNA helicases can be concealed by the stochastic behavior of enzyme molecules within the necessarily large populations used in ensemble experiments. With recent technological advances, the direct visualization of helicases acting on individual DNA molecules has contributed significantly to the current understanding of their mechanisms of action and biological functions. The combination of single-molecule techniques that enable both manipulation of individual protein or DNA molecules and visualization of their actions has made it possible to literally see novel and unique biochemical characteristics that were previously masked. Here, we describe the execution and use of single-molecule fluorescence imaging techniques, focusing on methods that include optical trapping in conjunction with epifluorescent imaging, and also surface immobilization in conjunction with total internal reflection fluorescence visualization. Combined with microchannel flow cells and microfluidic control, these methods allow individual fluorescently labeled protein and DNA molecules to be imaged and tracked, affording measurement of DNA unwinding and translocation at single-molecule resolution.
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Affiliation(s)
| | - J C Exell
- University of California, Davis, CA, United States
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12
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Seol Y, Strub MP, Neuman KC. Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis. Methods 2016; 105:119-27. [PMID: 27131595 PMCID: PMC4967025 DOI: 10.1016/j.ymeth.2016.04.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 01/26/2023] Open
Abstract
Magnetic tweezers is a versatile and easy to implement single-molecule technique that has become increasingly prevalent in the study of nucleic acid based molecular motors. Here, we provide a description of the magnetic tweezers instrument and guidelines for measuring and analyzing DNA helicase activity. Along with experimental methods, we describe a robust method of single-molecule trajectory analysis based on the Student's t-test that accommodates continuous transitions in addition to the discrete transitions assumed in most widely employed analysis routines. To illustrate the single-molecule unwinding assay and the analysis routine, we provide DNA unwinding measurements of Escherichia coli RecQ helicase under a variety of conditions (Na+, ATP, temperature, and DNA substrate geometry). These examples reveal that DNA unwinding measurements under various conditions can aid in elucidating the unwinding mechanism of DNA helicase but also emphasize that environmental effects on DNA helicase activity must be considered in relation to in vivo activity and mechanism.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Marie-Paule Strub
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA.
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Gyimesi M, Harami GM, Kocsis ZS, Kovács M. Recent adaptations of fluorescence techniques for the determination of mechanistic parameters of helicases and translocases. Methods 2016; 108:24-39. [PMID: 27133766 DOI: 10.1016/j.ymeth.2016.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 01/11/2023] Open
Abstract
Helicases and translocases are nucleic acid (NA)-based molecular motors that use the free energy liberated during the nucleoside triphosphate (NTP, usually ATP) hydrolysis cycle for unidirectional translocation along their NA (DNA, RNA or heteroduplex) substrates. Determination of the kinetic and thermodynamic parameters of their mechanoenzymatic cycle serves as a basis for the exploration of their physiological behavior and various cellular functions. Here we describe how recent adaptations of fluorescence-based solution kinetic methods can be used to determine practically all important mechanistic parameters of NA-based motor proteins. We outline practically useful analysis procedures for equilibrium, steady-state and transient kinetic data. This analysis can be used to quantitatively characterize the enzymatic steps of the NTP hydrolytic cycle, the binding site size, stoichiometry and energetics of protein-NA interactions, the rate and processivity of translocation along and unwinding of NA strands, and the mechanochemical coupling between these processes. The described methods yield insights into the functional role of the enzymes, and also greatly aid the design and interpretation of single-molecule experiments as well as the engineering of enzymatic properties for biotechnological applications.
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Affiliation(s)
- Máté Gyimesi
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Zsuzsa S Kocsis
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
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14
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Xie P. Dynamics of monomeric and hexameric helicases. Biophys Chem 2016; 211:49-58. [DOI: 10.1016/j.bpc.2016.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 01/19/2023]
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15
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Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding. Proc Natl Acad Sci U S A 2015; 112:E6852-61. [PMID: 26540728 DOI: 10.1073/pnas.1518028112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40-60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.
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16
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Harami GM, Nagy NT, Martina M, Neuman KC, Kovács M. The HRDC domain of E. coli RecQ helicase controls single-stranded DNA translocation and double-stranded DNA unwinding rates without affecting mechanoenzymatic coupling. Sci Rep 2015; 5:11091. [PMID: 26067769 PMCID: PMC4464074 DOI: 10.1038/srep11091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/05/2015] [Indexed: 01/01/2023] Open
Abstract
DNA-restructuring activities of RecQ-family helicases play key roles in genome maintenance. These activities, driven by two tandem RecA-like core domains, are thought to be controlled by accessory DNA-binding elements including the helicase-and-RnaseD-C-terminal (HRDC) domain. The HRDC domain of human Bloom’s syndrome (BLM) helicase was shown to interact with the RecA core, raising the possibility that it may affect the coupling between ATP hydrolysis, translocation along single-stranded (ss)DNA and/or unwinding of double-stranded (ds)DNA. Here, we determined how these activities are affected by the abolition of the ssDNA interaction of the HRDC domain or the deletion of the entire domain in E. coli RecQ helicase. Our data show that the HRDC domain suppresses the rate of DNA-activated ATPase activity in parallel with those of ssDNA translocation and dsDNA unwinding, regardless of the ssDNA binding capability of this domain. The HRDC domain does not affect either the processivity of ssDNA translocation or the tight coupling between the ATPase, translocation, and unwinding activities. Thus, the mechanochemical coupling of E. coli RecQ appears to be independent of HRDC-ssDNA and HRDC-RecA core interactions, which may play roles in more specialized functions of the enzyme.
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Affiliation(s)
- Gábor M Harami
- Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Nikolett T Nagy
- Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Máté Martina
- Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Keir C Neuman
- Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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Sarlós K, Gyimesi M, Kele Z, Kovács M. Mechanism of RecQ helicase mechanoenzymatic coupling reveals that the DNA interactions of the ADP-bound enzyme control translocation run terminations. Nucleic Acids Res 2014; 43:1090-7. [PMID: 25539922 PMCID: PMC4333385 DOI: 10.1093/nar/gku1333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The processing of various DNA structures by RecQ helicases is crucial for genome maintenance in both bacteria and eukaryotes. RecQ helicases perform active destabilization of DNA duplexes, based on tight coupling of their ATPase activity to moderately processive translocation along DNA strands. Here, we determined the ATPase kinetic mechanism of E. coli RecQ helicase to reveal how mechanoenzymatic coupling is achieved. We found that the interaction of RecQ with DNA results in a drastic acceleration of the rate-limiting ATP cleavage step, which occurs productively due to subsequent rapid phosphate release. ADP release is not rate-limiting and ADP-bound RecQ molecules make up a small fraction during single-stranded DNA translocation. However, the relatively rapid release of the ADP-bound enzyme from DNA causes the majority of translocation run terminations (i.e. detachment from the DNA track). Thus, the DNA interactions of ADP-bound RecQ helicase, probably dependent on DNA structure, will mainly determine translocation processivity and may control the outcome of DNA processing. Comparison with human Bloom's syndrome (BLM) helicase reveals that similar macroscopic parameters are achieved by markedly different underlying mechanisms of RecQ homologs, suggesting diversity in enzymatic tuning.
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Affiliation(s)
- Kata Sarlós
- Department of Biochemistry, ELTE-MTA 'Momentum' Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, Budapest, H-1117, Hungary
| | - Máté Gyimesi
- Department of Biochemistry, ELTE-MTA 'Momentum' Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, Budapest, H-1117, Hungary
| | - Zoltán Kele
- Department of Medical Chemistry, University of Szeged, Dóm sqr. 8. Szeged, H-6720, Hungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA 'Momentum' Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, Budapest, H-1117, Hungary
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18
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Kocsis ZS, Sarlós K, Harami GM, Martina M, Kovács M. A nucleotide-dependent and HRDC domain-dependent structural transition in DNA-bound RecQ helicase. J Biol Chem 2014; 289:5938-49. [PMID: 24403069 DOI: 10.1074/jbc.m113.530741] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The allosteric communication between the ATP- and DNA-binding sites of RecQ helicases enables efficient coupling of ATP hydrolysis to translocation along single-stranded DNA (ssDNA) and, in turn, the restructuring of multistranded DNA substrates during genome maintenance processes. In this study, we used the tryptophan fluorescence signal of Escherichia coli RecQ helicase to decipher the kinetic mechanism of the interaction of the enzyme with ssDNA. Rapid kinetic experiments revealed that ssDNA binding occurs in a two-step mechanism in which the initial binding step is followed by a structural transition of the DNA-bound helicase. We found that the nucleotide state of RecQ greatly influences the kinetics of the detected structural transition, which leads to a high affinity DNA-clamped state in the presence of the nucleotide analog ADP-AlF4. The DNA binding mechanism is largely independent of ssDNA length, indicating the independent binding of RecQ molecules to ssDNA and the lack of significant DNA end effects. The structural transition of DNA-bound RecQ was not detected when the ssDNA binding capability of the helicase-RNase D C-terminal domain was abolished or the domain was deleted. The results shed light on the nature of conformational changes leading to processive ssDNA translocation and multistranded DNA processing by RecQ helicases.
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Affiliation(s)
- Zsuzsa S Kocsis
- From the Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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19
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Abstract
Helicases have major roles in genome maintenance by unwinding structured nucleic acids. Their prominence is marked by various cancers and genetic disorders that are linked to helicase defects. Although considerable effort has been made to understand the functions of DNA helicases that are important for genomic stability and cellular homeostasis, the complexity of the DNA damage response leaves us with unanswered questions regarding how helicase-dependent DNA repair pathways are regulated and coordinated with cell cycle checkpoints. Further studies may open the door to targeting helicases in order to improve cancer treatments based on DNA-damaging chemotherapy or radiation.
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Affiliation(s)
- Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA.
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Ramanagoudr-Bhojappa R, Chib S, Byrd AK, Aarattuthodiyil S, Pandey M, Patel SS, Raney KD. Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA. J Biol Chem 2013; 288:16185-95. [PMID: 23596008 DOI: 10.1074/jbc.m113.470013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinetic analysis of the DNA unwinding and translocation activities of helicases is necessary for characterization of the biochemical mechanism(s) for this class of enzymes. Saccharomyces cerevisiae Pif1 helicase was characterized using presteady state kinetics to determine rates of DNA unwinding, displacement of streptavidin from biotinylated DNA, translocation on single-stranded DNA (ssDNA), and ATP hydrolysis activities. Unwinding of substrates containing varying duplex lengths was fit globally to a model for stepwise unwinding and resulted in an unwinding rate of ∼75 bp/s and a kinetic step size of 1 base pair. Pif1 is capable of displacing streptavidin from biotinylated oligonucleotides with a linear increase in the rates as the length of the oligonucleotides increased. The rate of translocation on ssDNA was determined by measuring dissociation from varying lengths of ssDNA and is essentially the same as the rate of unwinding of dsDNA, making Pif1 an active helicase. The ATPase activity of Pif1 on ssDNA was determined using fluorescently labeled phosphate-binding protein to measure the rate of phosphate release. The quantity of phosphate released corresponds to a chemical efficiency of 0.84 ATP/nucleotides translocated. Hence, when all of the kinetic data are considered, Pif1 appears to move along DNA in single nucleotide or base pair steps, powered by hydrolysis of 1 molecule of ATP.
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