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Alekseev A, Pobegalov G, Morozova N, Vedyaykin A, Cherevatenko G, Yakimov A, Baitin D, Khodorkovskii M. A new insight into RecA filament regulation by RecX from the analysis of conformation-specific interactions. eLife 2022; 11:78409. [PMID: 35730924 PMCID: PMC9252578 DOI: 10.7554/elife.78409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
RecA protein mediates homologous recombination repair in bacteria through assembly of long helical filaments on ssDNA in an ATP-dependent manner. RecX, an important negative regulator of RecA, is known to inhibit RecA activity by stimulating the disassembly of RecA nucleoprotein filaments. Here we use a single-molecule approach to address the regulation of (Escherichia coli) RecA-ssDNA filaments by RecX (E. coli) within the framework of distinct conformational states of RecA-ssDNA filament. Our findings revealed that RecX effectively binds the inactive conformation of RecA-ssDNA filaments and slows down the transition to the active state. Results of this work provide new mechanistic insights into the RecX-RecA interactions and highlight the importance of conformational transitions of RecA filaments as an additional level of regulation of its biological activity.
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Affiliation(s)
- Aleksandr Alekseev
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Natalia Morozova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Alexey Vedyaykin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Galina Cherevatenko
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Alexander Yakimov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Dmitry Baitin
- Kurchatov Institute, St. Petersburg, Russian Federation
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
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2
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Single-molecule characterization of compressed RecA nucleoprotein filaments. Biochem Biophys Res Commun 2022; 614:29-33. [PMID: 35567941 DOI: 10.1016/j.bbrc.2022.04.130] [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: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022]
Abstract
RecA is a central enzyme of homologous recombination in bacteria, which plays a major role in DNA repair, natural transformation and SOS-response activation. RecA forms nucleoprotein filaments on single-stranded DNA with a highly conserved architecture that is also shared by eukaryotic recombinases. One of the key features of these filaments is the ability to switch between stretched and compressed conformations in response to ATP binding and hydrolysis. However, the functional role of such conformational changes is not fully understood. Structural data revealed that in the absence of ATP RecA binds DNA with the stoichiometry of 5 nucleotides per one monomer, while in the presence of ATP the binding stoichiometry is 3:1. Such differences suggest incompatibility of the active and inactive conformations, yet dynamic single-molecule studies demonstrated that ATP and apo conformations can be directly interconvertible. In the present work we use a single-molecule approach to address the features of inactive RecA nucleoprotein filaments formed de novo in the absence of nucleotide cofactors. We show that compressed RecA-DNA filaments can exist with both 5:1 and 3:1 binding stoichiometry which is determined by conditions of the filament assembly. However, only a 3:1 stoichiometry allows direct interconvertibility with the active ATP-bound conformation.
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3
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Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA. Int J Mol Sci 2020; 21:ijms21197389. [PMID: 33036395 PMCID: PMC7583915 DOI: 10.3390/ijms21197389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 11/17/2022] Open
Abstract
Deinococcus radiodurans (Dr) has one of the most robust DNA repair systems, which is capable of withstanding extreme doses of ionizing radiation and other sources of DNA damage. DrRecA, a central enzyme of recombinational DNA repair, is essential for extreme radioresistance. In the presence of ATP, DrRecA forms nucleoprotein filaments on DNA, similar to other bacterial RecA and eukaryotic DNA strand exchange proteins. However, DrRecA catalyzes DNA strand exchange in a unique reverse pathway. Here, we study the dynamics of DrRecA filaments formed on individual molecules of duplex and single-stranded DNA, and we follow conformational transitions triggered by ATP hydrolysis. Our results reveal that ATP hydrolysis promotes rapid DrRecA dissociation from duplex DNA, whereas on single-stranded DNA, DrRecA filaments interconvert between stretched and compressed conformations, which is a behavior shared by E. coli RecA and human Rad51. This indicates a high conservation of conformational switching in nucleoprotein filaments and suggests that additional factors might contribute to an inverse pathway of DrRecA strand exchange.
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4
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Alekseev A, Serdakov M, Pobegalov G, Yakimov A, Bakhlanova I, Baitin D, Khodorkovskii M. Single-molecule analysis reveals two distinct states of the compressed RecA filament on single-stranded DNA. FEBS Lett 2020; 594:3464-3476. [PMID: 32880917 DOI: 10.1002/1873-3468.13922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 11/07/2022]
Abstract
The RecA protein plays a key role in bacterial homologous recombination (HR) and acts through assembly of long helical filaments around single-stranded DNA in the presence of ATP. Large-scale conformational changes induced by ATP hydrolysis result in transitions between stretched and compressed forms of the filament. Here, using a single-molecule approach, we show that compressed RecA nucleoprotein filaments can exist in two distinct interconvertible states depending on the presence of ADP in the monomer-monomer interface. Binding of ADP promotes cooperative conformational transitions and directly affects mechanical properties of the filament. Our findings reveal that RecA nucleoprotein filaments are able to continuously cycle between three mechanically distinct states that might have important implications for RecA-mediated processes of HR.
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Affiliation(s)
| | - Maksim Serdakov
- Peter the Great St Petersburg Polytechnic University, Russia
| | | | - Alexandr Yakimov
- Peter the Great St Petersburg Polytechnic University, Russia
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P. Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina, Russia
| | - Irina Bakhlanova
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P. Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina, Russia
| | - Dmitry Baitin
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P. Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St Petersburg Polytechnic University, Russia
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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5
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A Comprehensive View of Translesion Synthesis in Escherichia coli. Microbiol Mol Biol Rev 2020; 84:84/3/e00002-20. [PMID: 32554755 DOI: 10.1128/mmbr.00002-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The lesion bypass pathway, translesion synthesis (TLS), exists in essentially all organisms and is considered a pathway for postreplicative gap repair and, at the same time, for lesion tolerance. As with the saying "a trip is not over until you get back home," studying TLS only at the site of the lesion is not enough to understand the whole process of TLS. Recently, a genetic study uncovered that polymerase V (Pol V), a poorly expressed Escherichia coli TLS polymerase, is not only involved in the TLS step per se but also participates in the gap-filling reaction over several hundred nucleotides. The same study revealed that in contrast, Pol IV, another highly expressed TLS polymerase, essentially stays away from the gap-filling reaction. These observations imply fundamentally different ways these polymerases are recruited to DNA in cells. While access of Pol IV appears to be governed by mass action, efficient recruitment of Pol V involves a chaperone-like action of the RecA filament. We present a model of Pol V activation: the 3' tip of the RecA filament initially stabilizes Pol V to allow stable complex formation with a sliding β-clamp, followed by the capture of the terminal RecA monomer by Pol V, thus forming a functional Pol V complex. This activation process likely determines higher accessibility of Pol V than of Pol IV to normal DNA. Finally, we discuss the biological significance of TLS polymerases during gap-filling reactions: error-prone gap-filling synthesis may contribute as a driving force for genetic diversity, adaptive mutation, and evolution.
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Ousaka N, Shimizu K, Suzuki Y, Iwata T, Itakura M, Taura D, Iida H, Furusho Y, Mori T, Yashima E. Spiroborate-Based Double-Stranded Helicates: Meso-to-Racemo Isomerization and Ion-Triggered Springlike Motion of the Racemo-Helicate. J Am Chem Soc 2018; 140:17027-17039. [DOI: 10.1021/jacs.8b08268] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Naoki Ousaka
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Kaori Shimizu
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yoshimasa Suzuki
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Takuya Iwata
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Manabu Itakura
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Daisuke Taura
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroki Iida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yoshio Furusho
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Eiji Yashima
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
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Wright WD, Shah SS, Heyer WD. Homologous recombination and the repair of DNA double-strand breaks. J Biol Chem 2018; 293:10524-10535. [PMID: 29599286 DOI: 10.1074/jbc.tm118.000372] [Citation(s) in RCA: 406] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination enables the cell to access and copy intact DNA sequence information in trans, particularly to repair DNA damage affecting both strands of the double helix. Here, we discuss the DNA transactions and enzymatic activities required for this elegantly orchestrated process in the context of the repair of DNA double-strand breaks in somatic cells. This includes homology search, DNA strand invasion, repair DNA synthesis, and restoration of intact chromosomes. Aspects of DNA topology affecting individual steps are highlighted. Overall, recombination is a dynamic pathway with multiple metastable and reversible intermediates designed to achieve DNA repair with high fidelity.
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Affiliation(s)
| | | | - Wolf-Dietrich Heyer
- From the Departments of Microbiology and Molecular Genetics and .,Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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8
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TIRF-Based Single-Molecule Detection of the RecA Presynaptic Filament Dynamics. Methods Enzymol 2018; 600:233-253. [PMID: 29458760 DOI: 10.1016/bs.mie.2017.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RecA is a key protein in homologous DNA repair process. On a single-stranded (ss) DNA, which appears as an intermediate structure at a double-strand break site, RecA forms a kilobase-long presynaptic filament that mediates homology search and strand exchange reaction. RecA requires adenosine triphosphate as a cofactor that confers dynamic features to the filament such as nucleation, end-dependent growth and disassembly, scaffold shift along the ssDNA, and conformational change. Due to the complexity of the dynamics, detailed molecular mechanisms of functioning presynaptic filament have been characterized only recently after the advent of single-molecule techniques that allowed real-time observation of each kinetic process. In this chapter, single-molecule fluorescence resonance energy transfer assays, which revealed detailed molecular pictures of the presynaptic filament dynamics, will be discussed.
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Suzuki Y, Nakamura T, Iida H, Ousaka N, Yashima E. Allosteric Regulation of Unidirectional Spring-like Motion of Double-Stranded Helicates. J Am Chem Soc 2016; 138:4852-9. [DOI: 10.1021/jacs.6b00787] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yoshimasa Suzuki
- Department
of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Taiki Nakamura
- Department
of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroki Iida
- Department
of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Naoki Ousaka
- Department
of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Eiji Yashima
- Department
of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
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Kim SH, Ragunathan K, Park J, Joo C, Kim D, Ha T. Cooperative conformational transitions keep RecA filament active during ATPase cycle. J Am Chem Soc 2014; 136:14796-800. [PMID: 25252114 PMCID: PMC4210115 DOI: 10.1021/ja506363y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The active, stretched conformation of the RecA filament bound to single-stranded DNA is required for homologous recombination. During this process, the RecA filament mediates the homology search and base pair exchange with a complementary sequence. Subsequently, the RecA filament dissociates from DNA upon reaction completion. ATP binding and hydrolysis is critical throughout these processes. Little is known about the timescale, order of conversion between different cofactor bound forms during ATP hydrolysis, and the associated changes in filament conformation. We used single-molecule fluorescence techniques to investigate how ATP hydrolysis is coupled with filament dynamics. For the first time, we observed real-time cooperative structural changes within the RecA filament. This cooperativity between neighboring monomers provides a time window for nucleotide cofactor exchange, which keeps the filament in the active conformation amidst continuous cycles of ATP hydrolysis.
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Affiliation(s)
- Sung Hyun Kim
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University , Seoul 121-742, Korea
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11
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Ion-triggered spring-like motion of a double helicate accompanied by anisotropic twisting. Nat Chem 2010; 2:444-9. [DOI: 10.1038/nchem.649] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 03/23/2010] [Indexed: 11/09/2022]
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12
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Structural transitions within human Rad51 nucleoprotein filaments. Proc Natl Acad Sci U S A 2009; 106:12688-93. [PMID: 19622740 DOI: 10.1073/pnas.0811465106] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rad51 is a core component of the eukaryotic homologous recombination machinery and is responsible for key mechanistic steps during strand invasion. Higher order oligomers of Rad51 display a remarkable degree of structural variation, forming rings, compressed filaments, and elongated filaments. It is unclear whether Rad51 can transition directly between these different oligomeric structures without disassembling first into monomers. We have used single-molecule microscopy to investigate the behavior of human Rad51 assembled on double-stranded DNA. Our results show that human Rad51 can form elongated nucleoprotein filaments on DNA, but ATP hydrolysis causes a decrease in their length without concomitant dissociation of protein. Compressed Rad51 filaments can re-elongate when presented with either ATP or the non-hydrolyzable analog AMP-PNP, and these cycles of elongation and compression are reversible. A Rad51 mutant deficient in ATP hydrolysis is locked into an extended conformation that is incapable of transitioning to a compressed filament. Similarly, wild-type Rad51 bound to DNA in the presence of AMP-PNP was trapped in the elongated state. Proteins incapable of transitioning to the compressed state were also highly resistant to dissociation from the DNA. Taken together, our results indicate that nucleotide hydrolysis by human Rad51 triggers a reversible structural transition leading to filaments with reduced helical pitch.
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van Loenhout MTJ, van der Heijden T, Kanaar R, Wyman C, Dekker C. Dynamics of RecA filaments on single-stranded DNA. Nucleic Acids Res 2009; 37:4089-99. [PMID: 19429893 PMCID: PMC2709578 DOI: 10.1093/nar/gkp326] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RecA, the key protein in homologous recombination, performs its actions as a helical filament on single-stranded DNA (ssDNA). ATP hydrolysis makes the RecA-ssDNA filament dynamic and is essential for successful recombination. RecA has been studied extensively by single-molecule techniques on double-stranded DNA (dsDNA). Here we directly probe the structure and kinetics of RecA interaction with its biologically most relevant substrate, long ssDNA molecules. We find that RecA ATPase activity is required for the formation of long continuous filaments on ssDNA. These filaments both nucleate and extend with a multimeric unit as indicated by the Hill coefficient of 5.4 for filament nucleation. Disassembly rates of RecA from ssDNA decrease with applied stretching force, corresponding to a mechanism where protein-induced stretching of the ssDNA aids in the disassembly. Finally, we show that RecA-ssDNA filaments can reversibly interconvert between an extended, ATP-bound, and a compressed, ADP-bound state. Taken together, our results demonstrate that ATP hydrolysis has a major influence on the structure and state of RecA filaments on ssDNA.
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Affiliation(s)
- Marijn T J van Loenhout
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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Finkelstein IJ, Greene EC. Single molecule studies of homologous recombination. MOLECULAR BIOSYSTEMS 2008; 4:1094-104. [PMID: 18931785 DOI: 10.1039/b811681b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Single molecule methods offer an unprecedented opportunity to examine complex macromolecular reactions that are obfuscated by ensemble averaging. The application of single molecule techniques to study DNA processing enzymes has revealed new mechanistic details that are unobtainable from bulk biochemical studies. Homologous DNA recombination is a multi-step pathway that is facilitated by numerous enzymes that must precisely and rapidly manipulate diverse DNA substrates to repair potentially lethal breaks in the DNA duplex. In this review, we present an overview of single molecule assays that have been developed to study key aspects of homologous recombination and discuss the unique information gleaned from these experiments.
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Affiliation(s)
- Ilya J Finkelstein
- Departments of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA
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