1
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Lee AJ, Endo M, Hobbs JK, Davies AG, Wälti C. Micro-homology intermediates: RecA's transient sampling revealed at the single molecule level. Nucleic Acids Res 2021; 49:1426-1435. [PMID: 33476368 PMCID: PMC7897476 DOI: 10.1093/nar/gkaa1258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 12/12/2020] [Accepted: 01/07/2021] [Indexed: 01/21/2023] Open
Abstract
Recombinase A (RecA) is central to homologous recombination. However, despite significant advances, the mechanism with which RecA is able to orchestrate a search for homology remains elusive. DNA nanostructure-augmented high-speed AFM offers the spatial and temporal resolutions required to study the RecA recombination mechanism directly and at the single molecule level. We present the direct in situ observation of RecA-orchestrated alignment of homologous DNA strands to form a stable recombination product within a supporting DNA nanostructure. We show the existence of subtle and short-lived states in the interaction landscape, which suggests that RecA transiently samples micro-homology at the single RecA monomer-level throughout the search for sequence alignment. These transient interactions form the early steps in the search for sequence homology, prior to the formation of stable pairings at >8 nucleotide seeds. The removal of sequence micro-homology results in the loss of the associated transient sampling at that location.
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Affiliation(s)
- Andrew J Lee
- Bioelectronics, The Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Woodhouse lane, Leeds LS2 9JT, UK
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jamie K Hobbs
- Department of Physics and Astronomy, University of Sheffield, Houndsfield Road, Sheffield S3 7RH, UK
| | - A Giles Davies
- Bioelectronics, The Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Woodhouse lane, Leeds LS2 9JT, UK
| | - Christoph Wälti
- Bioelectronics, The Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Woodhouse lane, Leeds LS2 9JT, UK
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2
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Maslowska KH, Makiela‐Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:368-384. [PMID: 30447030 PMCID: PMC6590174 DOI: 10.1002/em.22267] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 05/10/2023]
Abstract
Genomes of all living organisms are constantly threatened by endogenous and exogenous agents that challenge the chemical integrity of DNA. Most bacteria have evolved a coordinated response to DNA damage. In Escherichia coli, this inducible system is termed the SOS response. The SOS global regulatory network consists of multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage at the cost of elevated mutagenesis. Due to its mutagenic potential, the SOS response is subject to elaborate regulatory control involving not only transcriptional derepression, but also post-translational activation, and inhibition. This review summarizes current knowledge about the molecular mechanism of the SOS response induction and progression and its consequences for genome stability. Environ. Mol. Mutagen. 60:368-384, 2019. © 2018 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Katarzyna H. Maslowska
- Cancer Research Center of Marseille, CNRS, UMR7258Inserm, U1068; Institut Paoli‐Calmettes, Aix‐Marseille UniversityMarseilleFrance
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | | | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
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3
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Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation. BMC Genomics 2018; 19:373. [PMID: 29783948 PMCID: PMC5963079 DOI: 10.1186/s12864-018-4716-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/23/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.
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Affiliation(s)
- Evelyne Krin
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Sebastian Aguilar Pierlé
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Odile Sismeiro
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Bernd Jagla
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Biomarker Discovery Platform, UtechS CB and Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Marie-Agnès Dillies
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Oihane Irazoki
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Susana Campoy
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Zoé Rouy
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Stéphane Cruveiller
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Claudine Médigue
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Jean-Yves Coppée
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Didier Mazel
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
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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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5
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Kim SH, Ahn T, Cui TJ, Chauhan S, Sung J, Joo C, Kim D. RecA filament maintains structural integrity using ATP-driven internal dynamics. SCIENCE ADVANCES 2017; 3:e1700676. [PMID: 28913424 PMCID: PMC5587095 DOI: 10.1126/sciadv.1700676] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
At the core of homologous DNA repair, RecA catalyzes the strand exchange reaction. This process is initiated by a RecA loading protein, which nucleates clusters of RecA proteins on single-stranded DNA. Each cluster grows to cover the single-stranded DNA but may leave 1- to 2-nucleotide (nt) gaps between the clusters due to three different structural phases of the nucleoprotein filaments. It remains to be revealed how RecA proteins eliminate the gaps to make a seamless kilobase-long filament. We develop a single-molecule fluorescence assay to observe the novel internal dynamics of the RecA filament. We directly observe the structural phases of individual RecA filaments and find that RecA proteins move their positions along the substrate DNA to change the phase of the filament. This reorganization process, which is a prerequisite step for interjoining of two adjacent clusters, requires adenosine triphosphate hydrolysis and is tightly regulated by the recombination hotspot, Chi. Furthermore, RecA proteins recognize and self-align to a 3-nt-period sequence pattern of TGG. This sequence-dependent phase bias may help the RecA filament to maintain structural integrity within the kilobase-long filament for accurate homology search and strand exchange reaction.
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Affiliation(s)
- Sung Hyun Kim
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
- Department of Bionanoscience, Kavli Institute of NanoScience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - TakKyoon Ahn
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Tao Ju Cui
- Department of Bionanoscience, Kavli Institute of NanoScience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Sweeny Chauhan
- Department of Bionanoscience, Kavli Institute of NanoScience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Jaeyoung Sung
- Department of Chemistry, Chung-Ang University, Seoul, Republic of Korea
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of NanoScience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Doseok Kim
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
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6
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Enhancement of RecA-mediated self-assembly in DNA nanostructures through basepair mismatches and single-strand nicks. Sci Rep 2017; 7:41081. [PMID: 28112216 PMCID: PMC5253629 DOI: 10.1038/srep41081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/14/2016] [Indexed: 12/16/2022] Open
Abstract
The use of DNA as a structural material for nanometre-scale construction has grown extensively over the last decades. The development of more advanced DNA-based materials would benefit from a modular approach enabling the direct assembly of additional elements onto nanostructures after fabrication. RecA-based nucleoprotein filaments encapsulating short ssDNA have been demonstrated as a tool for highly efficient and fully programmable post-hoc patterning of duplex DNA scaffold. However, the underlying assembly process is not fully understood, in particular when patterning complex DNA topologies. Here, we report the effect of basepair-mismatched regions and single-strand nicks in the double-stranded DNA scaffold on the yield of RecA-based assembly. Significant increases in assembly yield are observed upon the introduction of unpaired basepairs directly adjacent to the assembly region. However, when the unpaired regions were introduced further from the assembly site the assembly yield initially decreased as the length of the unpaired region was increased. These results suggest that an unpaired region acts as a kinetic trap for RecA-based nucleoprotein filaments, impeding the assembly mechanism. Conversely, when the unpaired region is located directly adjacent to the assembly site, it leads to an increase in efficiency of RecA patterning owing to increased breathing of the assembly site.
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7
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Chandran AV, Jayanthi S, Vijayan M. Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:98-111. [PMID: 28049371 DOI: 10.1080/07391102.2016.1268975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from Mycobacterium tuberculosis, Mycobacterium smegmatis and Escherichia coli and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles. The simulations indicate the possibility of additional interactions involving the P-loop which remains largely invariant. The phosphate tail of the ATP is firmly anchored on the loop while the nucleoside moiety exhibits substantial structural variability. The most important consequence of ATP binding is the movement of the 'switch' residue. The relevant simulations indicate the feasibility of a second nucleotide binding site, but the pathway between adjacent molecules in the filament involving the two nucleotide binding sites appears to be possible only in the mycobacterial proteins.
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Affiliation(s)
- Anu V Chandran
- a Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - S Jayanthi
- a Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - M Vijayan
- a Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
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8
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Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Çakır A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8403-8412. [PMID: 27479732 DOI: 10.1021/acs.langmuir.6b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
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Affiliation(s)
| | | | | | - Joshua Araya
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Philip Nevin
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Erik Werner
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Ali Çakır
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Fredrik Persson
- Department for Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , 751 24 Uppsala, Sweden
| | - Edwige B Garcin
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
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9
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Schay G, Borka B, Kernya L, Bulyáki É, Kardos J, Fekete M, Fidy J. Without Binding ATP, Human Rad51 Does Not Form Helical Filaments on ssDNA. J Phys Chem B 2016; 120:2165-78. [PMID: 26890079 DOI: 10.1021/acs.jpcb.5b12220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of the presynaptic filament (PSF) of proper helical structure by Rad51 recombinases is a prerequisite of the progress of homologous recombination repair. We studied the contribution of ATP-binding to this structure of wt human Rad51 (hRad51). We exploited the protein-dissociation effect of high hydrostatic pressure to determine the free energy of dissociation of the protomer interfaces in hRad51 oligomer states and used electron microscopy to obtain topological parameters. Without cofactors ATP and Ca(2+) and template DNA, hRad51 did not exist in monomer form, but it formed rodlike long filaments without helical order. ΔG(diss) indicated a strong inherent tendency of aggregation. Binding solely ssDNA left the filament unstructured with slightly increased ΔG(diss). Adding only ATP and Ca(2+) to the buffer disintegrated the self-associated rods into rings and short helices of further increased ΔG(diss). Rad51 binding to ssDNA only with ATP and Ca bound could lead to ordered helical filament formation of proper pitch size with interface contacts of K(d) ∼ 2 × 10(-11) M, indicating a structure of outstanding stability. ATP/Ca binding increased the ΔG(diss) of protomer contacts in the filament by 16 kJ/mol. The results emphasize that ATP-binding in the PSF of hRad51 has an essential, yet purely structural, role.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Bálint Borka
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Linda Kernya
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Éva Bulyáki
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Melinda Fekete
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
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10
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Chandran AV, Prabu JR, Nautiyal A, Patil KN, Muniyappa K, Vijayan M. Structural studies on Mycobacterium tuberculosis RecA: molecular plasticity and interspecies variability. J Biosci 2015; 40:13-30. [PMID: 25740138 DOI: 10.1007/s12038-014-9497-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP is central for all the biochemical activities of RecA. The strengths of interaction of the ligands with the P-loop reveal significant differences. This in turn affects the magnitude of the motion of the 'switch' residue, Gln195 in M. tuberculosis RecA, which triggers the transmission of ATP-mediated allosteric information to the DNA binding region. M. tuberculosis RecA is substantially rigid compared with its counterparts from M. smegmatis and E. coli, which exhibit concerted internal molecular mobility. The interspecies variability in the plasticity of the two mycobacterial proteins is particularly surprising as they have similar sequence and 3D structure. Details of the interactions of ligands with the protein, characterized in the structures reported here, could be useful for design of inhibitors against M. tuberculosis RecA.
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Affiliation(s)
- Anu V Chandran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012
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11
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Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert CH, Prévost C. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. PLoS One 2015; 10:e0116414. [PMID: 25785454 PMCID: PMC4364692 DOI: 10.1371/journal.pone.0116414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Oligomeric macromolecules in the cell self-organize into a wide variety of geometrical motifs such as helices, rings or linear filaments. The recombinase proteins involved in homologous recombination present many such assembly motifs. Here, we examine in particular the polymorphic characteristics of RecA, the most studied member of the recombinase family, using an integrative approach that relates local modes of monomer/monomer association to the global architecture of their screw-type organization. In our approach, local modes of association are sampled via docking or Monte Carlo simulations. This enables shedding new light on fiber morphologies that may be adopted by the RecA protein. Two distinct RecA helical morphologies, the so-called "extended" and "compressed" forms, are known to play a role in homologous recombination. We investigate the variability within each form in terms of helical parameters and steric accessibility. We also address possible helical discontinuities in RecA filaments due to multiple monomer-monomer association modes. By relating local interface organization to global filament morphology, the strategies developed here to study RecA self-assembly are particularly well suited to other DNA-binding proteins and to filamentous protein assemblies in general.
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Affiliation(s)
- Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Johann Ezelin
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pierre Poulain
- DSIMB team, Inserm UMR-S 665 and Univ. Paris Diderot, Sorbonne Paris Cité, INTS, 6 rue Alexandre Cabanel, 75015 Paris, France
- Ets Poulain, Pointe-Noire, Republic of Congo
| | - Adrien Saladin
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Martin Zacharias
- Technische Universität München, Physik-Department, James-Franck-Str. 1, 85748 Garching, Germany
| | - Charles H. Robert
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- * E-mail:
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12
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Kim SH, Park J, Joo C, Kim D, Ha T. Dynamic growth and shrinkage govern the pH dependence of RecA filament stability. PLoS One 2015; 10:e0115611. [PMID: 25608006 PMCID: PMC4301630 DOI: 10.1371/journal.pone.0115611] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 11/30/2014] [Indexed: 11/19/2022] Open
Abstract
RecA proteins form a long stable filament on a single-stranded DNA and catalyze strand exchange reaction. The stability of RecA filament changes dramatically with pH, yet its detailed mechanism is not known. Here, using a single molecule assay, we determined the binding and dissociation rates of RecA monomers at the filament ends at various pH. The pH-induced rate changes were moderate but occurred in opposite directions for binding and dissociation, resulting in a substantial increase in filament stability in lower pH. The highly charged residues in C-terminal domain do not contribute to the pH dependent stability. The stability enhancement of RecA filament in low pH may help the cell to cope with acidic stress by fine-tuning of the binding and dissociation rates without losing the highly dynamic nature of the filament required for strand exchange.
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Affiliation(s)
- Sung Hyun Kim
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Korea
| | - Jeehae Park
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands
| | - Doseok Kim
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Korea
- * E-mail: (TH); (DK)
| | - Taekjip Ha
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Howard Hughes Medical Institute, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (TH); (DK)
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13
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Frykholm K, Alizadehheidari M, Fritzsche J, Wigenius J, Modesti M, Persson F, Westerlund F. Probing physical properties of a DNA-protein complex using nanofluidic channels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:884-7. [PMID: 24382826 DOI: 10.1002/smll.201302028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/08/2013] [Indexed: 05/28/2023]
Abstract
A method to investigate physical properties of a DNA-protein complex in solution is demonstrated. By using tapered nanochannels and lipid passivation the persistence length of a RecA filament formed on double-stranded DNA is determined to 1.15 μm, in agreement with the literature, without attaching protein or DNA to any handles or surfaces.
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Affiliation(s)
- Karolin Frykholm
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
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14
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Kim SH, Joo C, Ha T, Kim D. Molecular mechanism of sequence-dependent stability of RecA filament. Nucleic Acids Res 2013; 41:7738-44. [PMID: 23804763 PMCID: PMC3763553 DOI: 10.1093/nar/gkt570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
RecA is a DNA-dependent ATPase and mediates homologous recombination by first forming a filament on a single-stranded (ss) DNA. RecA binds preferentially to TGG repeat sequence, which resembles the recombination hot spot Chi (5′-GCTGGTGG-3′) and is the most frequent pattern (GTG) of the codon usage in Escherichia coli. Because of the highly dynamic nature of RecA filament formation, which consists of filament nucleation, growth and shrinkage, we need experimental approaches that can resolve each of these processes separately to gain detailed insights into the molecular mechanism of sequence preference. By using a single-molecule fluorescence assay, we examined the effect of sequence on individual stages of nucleation, monomer binding and dissociation. We found that RecA does not recognize the Chi sequence as a nucleation site. In contrast, we observed that it is the reduced monomer dissociation that mainly determines the high filament stability on TGG repeats. This sequence dependence of monomer dissociation is well-correlated with that of ATP hydrolysis, suggesting that DNA sequence dictates filament stability through modulation of ATP hydrolysis.
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Affiliation(s)
- Sung Hyun Kim
- Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea, Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands, Department of Physics and Center for the Physics of Living Cells, Institute for Genomic Biology and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Howard Hughes Medical Institute, Urbana, IL 61801, USA
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15
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Ngo KV, Molzberger ET, Chitteni-Pattu S, Cox MM. Regulation of Deinococcus radiodurans RecA protein function via modulation of active and inactive nucleoprotein filament states. J Biol Chem 2013; 288:21351-21366. [PMID: 23729671 DOI: 10.1074/jbc.m113.459230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RecA protein of Deinococcus radiodurans (DrRecA) has a central role in genome reconstitution after exposure to extreme levels of ionizing radiation. When bound to DNA, filaments of DrRecA protein exhibit active and inactive states that are readily interconverted in response to several sets of stimuli and conditions. At 30 °C, the optimal growth temperature, and at physiological pH 7.5, DrRecA protein binds to double-stranded DNA (dsDNA) and forms extended helical filaments in the presence of ATP. However, the ATP is not hydrolyzed. ATP hydrolysis of the DrRecA-dsDNA filament is activated by addition of single-stranded DNA, with or without the single-stranded DNA-binding protein. The ATPase function of DrRecA nucleoprotein filaments thus exists in an inactive default state under some conditions. ATPase activity is thus not a reliable indicator of DNA binding for all bacterial RecA proteins. Activation is effected by situations in which the DNA substrates needed to initiate recombinational DNA repair are present. The inactive state can also be activated by decreasing the pH (protonation of multiple ionizable groups is required) or by addition of volume exclusion agents. Single-stranded DNA-binding protein plays a much more central role in DNA pairing and strand exchange catalyzed by DrRecA than is the case for the cognate proteins in Escherichia coli. The data suggest a mechanism to enhance the efficiency of recombinational DNA repair in the context of severe genomic degradation in D. radiodurans.
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Affiliation(s)
- Khanh V Ngo
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Eileen T Molzberger
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Sindhu Chitteni-Pattu
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael M Cox
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706.
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16
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Atwell S, Disseau L, Stasiak AZ, Stasiak A, Renodon-Cornière A, Takahashi M, Viovy JL, Cappello G. Probing Rad51-DNA interactions by changing DNA twist. Nucleic Acids Res 2012. [PMID: 23180779 PMCID: PMC3526263 DOI: 10.1093/nar/gks1131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In eukaryotes, Rad51 protein is responsible for the recombinational repair of double-strand DNA breaks. Rad51 monomers cooperatively assemble on exonuclease-processed broken ends forming helical nucleo-protein filaments that can pair with homologous regions of sister chromatids. Homologous pairing allows the broken ends to be reunited in a complex but error-free repair process. Rad51 protein has ATPase activity but its role is poorly understood, as homologous pairing is independent of adenosine triphosphate (ATP) hydrolysis. Here we use magnetic tweezers and electron microscopy to investigate how changes of DNA twist affect the structure of Rad51-DNA complexes and how ATP hydrolysis participates in this process. We show that Rad51 protein can bind to double-stranded DNA in two different modes depending on the enforced DNA twist. The stretching mode is observed when DNA is unwound towards a helical repeat of 18.6 bp/turn, whereas a non-stretching mode is observed when DNA molecules are not permitted to change their native helical repeat. We also show that the two forms of complexes are interconvertible and that by enforcing changes of DNA twist one can induce transitions between the two forms. Our observations permit a better understanding of the role of ATP hydrolysis in Rad51-mediated homologous pairing and strand exchange.
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Affiliation(s)
- Scott Atwell
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
| | - Ludovic Disseau
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
| | - Alicja Z. Stasiak
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
| | - Andrzej Stasiak
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
- *To whom correspondence should be addressed. Tel: +41 21 692 4282; Fax: +41 21 692 4115;
| | - Axelle Renodon-Cornière
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
| | - Masayuki Takahashi
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
| | - Jean-Louis Viovy
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
| | - Giovanni Cappello
- Institut Curie, Centre de Recherche-Physico-Chimie-Curie, CNRS UMR168, Université Pierre et Marie Curie, Paris F-75231, France, Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland and Unité Fonctionnalité et Ingénierie des Protéines, FRE CNRS 3478, Université de Nantes, Nantes F-44322 Cedex 03, France
- Correspondence may also be addressed to Giovanni Cappello. Tel: +33 1 56 24 64 68; Fax: +33 1 40 51 06 36;
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17
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Chi P, Kwon Y, Visnapuu ML, Lam I, Santa Maria SR, Zheng X, Epshtein A, Greene EC, Sung P, Klein HL. Analyses of the yeast Rad51 recombinase A265V mutant reveal different in vivo roles of Swi2-like factors. Nucleic Acids Res 2011; 39:6511-22. [PMID: 21558173 PMCID: PMC3159464 DOI: 10.1093/nar/gkr297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Saccharomyces cerevisiae Swi2-like factors Rad54 and Rdh54 play multifaceted roles in homologous recombination via their DNA translocase activity. Aside from promoting Rad51-mediated DNA strand invasion of a partner chromatid, Rad54 and Rdh54 can remove Rad51 from duplex DNA for intracellular recycling. Although the in vitro properties of the two proteins are similar, differences between the phenotypes of the null allele mutants suggest that they play different roles in vivo. Through the isolation of a novel RAD51 allele encoding a protein with reduced affinity for DNA, we provide evidence that Rad54 and Rdh54 have different in vivo interactions with Rad51. The mutant Rad51 forms a complex on duplex DNA that is more susceptible to dissociation by Rdh54. This Rad51 variant distinguishes the in vivo functions of Rad54 and Rdh54, leading to the conclusion that two translocases remove Rad51 from different substrates in vivo. Additionally, we show that a third Swi2-like factor, Uls1, contributes toward Rad51 clearance from chromatin in the absence of Rad54 and Rdh54, and define a hierarchy of action of the Swi2-like translocases for chromosome damage repair.
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Affiliation(s)
- Peter Chi
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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18
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Lien CH, Wei MT, Tseng TY, Lee CD, Wang C, Wang TF, Ou-Yang HD, Chiou A. Probing the dynamic differential stiffness of dsDNA interacting with RecA in the enthalpic regime. OPTICS EXPRESS 2009; 17:20376-20385. [PMID: 19997266 DOI: 10.1364/oe.17.020376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
RecA plays a central role in homologous recombination of DNA. When RecA combines with dsDNA to form RecA-dsDNA nucleofilament, it unwinds dsDNA and changes its structure. The unwinding length extension of a DNA segment interacting with RecA has been studied by various techniques, but the dynamic differential stiffness of dsDNA conjugating with RecA has not been well characterized. We applied oscillatory optical tweezers to measure the differential stiffness of dsDNA molecules, interacting with RecA, as a function of time at a constant stretching force of 33.6pN. The values of the differential stiffness of DNA (for stretching force in the range of 20.0pN to 33.6pN) measured by oscillatory optical tweezers, both before and after its interaction with RecA, are consistent with those measured by stationary optical tweezers. In the dynamic measurement, we have shown that the association (or binding) rate increases with higher concentration of RecA; besides, we have also monitored in real-time the dissociation of RecA from the stretched RecA-dsDNA filament as ATPgammaS was washed off from the sample chamber. Finally, we verified that RecA (I26C), a form of RecA mutant, does not affect the differential stiffness of the stretched DNA sample. It implies that mutant RecA (I26C) does not bind to the DNA, which is consistent with the result obtained by conventional biochemical approach.
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Affiliation(s)
- Chia-Hui Lien
- Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
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19
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Smeets RMM, Kowalczyk SW, Hall AR, Dekker NH, Dekker C. Translocation of RecA-coated double-stranded DNA through solid-state nanopores. NANO LETTERS 2009; 9:3089-3096. [PMID: 19053490 DOI: 10.1021/nl803189k] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report translocation of double-stranded DNA (dsDNA) molecules that are coated with RecA protein through solid-state nanopores. Translocation measurements show current-blockade events with a wide variety in time duration (10-4-10-1 s) and conductance blockade values (3-14 nS). Large blockades (11.4+/-0.7 nS) are identified as being caused by translocations of RecA-dsDNA filaments. We confirm these results through a variety of methods, including changing molecular length and using an optical tweezer system to deliver bead-functionalized molecules to the nanopore. We further distinguish two different regimes of translocation: a low-voltage regime (<150 mV) in which the event rate increases exponentially with voltage, and a high-voltage regime in which it remains constant. Our results open possibilities for a variety of future experiments with (partly) protein-coated DNA molecules, which is interesting for both fundamental science and genomic screening applications.
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Affiliation(s)
- R M M Smeets
- KaVli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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20
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Abstract
The bacterial RecA protein participates in a remarkably diverse set of functions, all of which are involved in the maintenance of genomic integrity. RecA is a central component in both the catalysis of recombinational DNA repair and the regulation of the cellular SOS response. Despite the mechanistic differences of its functions, all require formation of an active RecA/ATP/DNA complex. RecA is a classic allosterically regulated enzyme, and ATP binding results in a dramatic increase in DNA binding affinity and a cooperative assembly of RecA subunits to form an ordered, helical nucleoprotein filament. The molecular events that underlie this ATP-induced structural transition are becoming increasingly clear. This review focuses on descriptions of our current understanding of the molecular design and allosteric regulation of RecA. We present a comprehensive list of all published recA mutants and use the results of various genetic and biochemical studies, together with available structural information, to develop ideas regarding the design of RecA functional domains and their catalytic organization.
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Affiliation(s)
- Dharia A McGrew
- Department of Biochemistry and Molecular Pharmacology, Aaron Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA
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21
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Gruenig MC, Renzette N, Long E, Chitteni-Pattu S, Inman RB, Cox MM, Sandler SJ. RecA-mediated SOS induction requires an extended filament conformation but no ATP hydrolysis. Mol Microbiol 2008; 69:1165-79. [PMID: 18627467 DOI: 10.1111/j.1365-2958.2008.06341.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Escherichia coli SOS response to DNA damage is modulated by the RecA protein, a recombinase that forms an extended filament on single-stranded DNA and hydrolyzes ATP. The RecA K72R (recA2201) mutation eliminates the ATPase activity of RecA protein. The mutation also limits the capacity of RecA to form long filaments in the presence of ATP. Strains with this mutation do not undergo SOS induction in vivo. We have combined the K72R variant of RecA with another mutation, RecA E38K (recA730). In vitro, the double mutant RecA E38K/K72R (recA730,2201) mimics the K72R mutant protein in that it has no ATPase activity. The double mutant protein will form long extended filaments on ssDNA and facilitate LexA cleavage almost as well as wild-type, and do so in the presence of ATP. Unlike recA K72R, the recA E38K/K72R double mutant promotes SOS induction in vivo after UV treatment. Thus, SOS induction does not require ATP hydrolysis by the RecA protein, but does require formation of extended RecA filaments. The RecA E38K/K72R protein represents an improved reagent for studies of the function of ATP hydrolysis by RecA in vivo and in vitro.
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Affiliation(s)
- Marielle C Gruenig
- Department of Biochemistry, 433 Babcock Drive, University of Wisconsin, Madison, WI 53706, USA
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22
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Singleton SF, Roca AI, Lee AM, Xiao J. Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog. Tetrahedron 2007; 63:3553-3566. [PMID: 17955055 PMCID: PMC2031864 DOI: 10.1016/j.tet.2006.10.092] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The RecA protein of Escherichia coli plays a crucial roles in DNA recombination and repair, as well as various aspects of bacterial pathogenicity. The formation of a RecA-ATP-ssDNA complex initiates all RecA activities and yet a complete structural and mechanistic description of this filament has remained elusive. An analysis of RecA-DNA interactions was performed using fluorescently labeled oligonucleotides. A direct comparison was made between fluorescein and several fluorescent nucleosides. The fluorescent guanine analog 6-methylisoxanthopterin (6MI) demonstrated significant advantages over the other fluorophores and represents an important new tool for characterizing RecA-DNA interactions.
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Affiliation(s)
- Scott F. Singleton
- Division of Medicinal Chemistry & Natural Products, School of Pharmacy, The University of North Carolina at Chapel Hill, CB 7360, Chapel Hill, NC 27599-7360, USA
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23
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Krishna R, Prabu JR, Manjunath GP, Datta S, Chandra NR, Muniyappa K, Vijayan M. Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA. J Mol Biol 2007; 367:1130-44. [PMID: 17306300 DOI: 10.1016/j.jmb.2007.01.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/17/2007] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all in space group P6(1). They include one obtained by reducing relative humidity around the crystal. In all crystals, RecA monomers form filaments around a 6(1) screw axis. Thus, the c-dimension of the crystal corresponds to the pitch of the RecA filament. As reported for Escherichia coli RecA, the variation in the pitch among the three forms correlates well with the motion of the C-terminal domain of the RecA monomers with respect to the main domain. The domain motion is compatible with formation of inactive as well as active RecA filaments involving monomers with a fully ordered C domain. It does not appear to influence the movement upon nucleotide-binding of the switch residue, which is believed to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding region. Interestingly, partial dehydration of the crystal results in the movement of the residue similar to that caused by nucleotide binding. The ordering of the DNA-binding loops, which present ensembles of conformations, is also unaffected by domain motion. The conformation of loop L2 appears to depend upon nucleotide binding, presumably on account of the movement of the switch residue that forms part of the loop. The conformations of loops L1 and L2 are correlated and have implications for intermolecular communications within the RecA filament. The structures resulting from different orientations of the C domain and different conformations of the DNA-binding loops appear to represent snapshots of the RecA at different phases of activity, and provide insights into the mechanism of action of RecA.
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Affiliation(s)
- R Krishna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
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24
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The bacterial RecA protein: structure, function, and regulation. MOLECULAR GENETICS OF RECOMBINATION 2007. [DOI: 10.1007/978-3-540-71021-9_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination. Although much is known about the structure of RecA protein itself, we do not at present have a detailed picture of how RecA binds to ssDNA and dsDNA substrates, and how these interactions are controlled by the binding and hydrolysis of the ATP cofactor. Recent studies from electron microscopy and X-ray crystallography have revealed important ATP-mediated conformational changes that occur within the protein, providing new insights into how RecA catalyses DNA strand-exchange. A unifying theme is emerging for RecA and related ATPase enzymes in which the binding of ATP at a subunit interface results in large conformational changes that are coupled to interactions with the substrates in such a way as to promote the desired reactions.
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Affiliation(s)
- Charles E Bell
- Department of Molecular and Cellular Biochemistry, Ohio State University College of Medicine and Public Health, 371 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA.
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26
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Shi WX, Larson RG. Atomic force microscopic study of aggregation of RecA-DNA nucleoprotein filaments into left-handed supercoiled bundles. NANO LETTERS 2005; 5:2476-81. [PMID: 16351198 DOI: 10.1021/nl051783v] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
RecA and its complexes with double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) are responsible for homologous recombination and DNA repair. In this study, we have observed, by atomic force microscopy (AFM), two-filament left-handed superhelices of RecA-dsDNA filaments that further interwind into four- or six-filament bundles, in addition to previously reported left-handed bundles of three or six filaments. Also revealed are four-filament bundles formed by further interwinding of two intrafilament superhelices of individual filaments. Pitches of superhelices of RecA-DNA filaments are similar to each other regardless the number of component filaments, and those formed on Phix174 RFII dsDNA and pNEB206A dsDNA are measured as 339.3 +/- 6.2 nm (690 counts of pitch/2) and 321.6 +/- 11.7 nm (101 counts of pitch/2), respectively, consistent with earlier measurements made by electron microscopy with a much smaller sample size. The study of these structures provides insight into the self-interactions of RecA and RecA-like proteins, which are present in all living cells, and into the general phenomenon of bundling, which is relevant to both biological and nonbiological filaments.
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Affiliation(s)
- Wei-Xian Shi
- Department of Chemical Engineering, University of Michigan, 3074 H.H. Dow, 2300 Hayward Street, Ann Arbor, MI 48109-2136, USA
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27
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Rajan R, Bell CE. Crystal structure of RecA from Deinococcus radiodurans: insights into the structural basis of extreme radioresistance. J Mol Biol 2005; 344:951-63. [PMID: 15544805 DOI: 10.1016/j.jmb.2004.09.087] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/27/2004] [Accepted: 09/28/2004] [Indexed: 11/15/2022]
Abstract
The resistance of Deinococcus radiodurans (Dr) to extreme doses of ionizing radiation depends on its highly efficient capacity to repair dsDNA breaks. Dr RecA, the key protein in the repair of dsDNA breaks by homologous recombination, promotes DNA strand-exchange by an unprecedented inverse pathway, in which the presynaptic filament is formed on dsDNA instead of ssDNA. In order to gain insight into the remarkable repair capacity of Dr and the novel mechanistic features of its RecA protein, we have determined its X-ray crystal structure in complex with ATPgammaS at 2.5A resolution. Like RecA from Escherichia coli, Dr RecA crystallizes as a helical filament that is closely related to its biologically relevant form, but with a more compressed pitch of 67 A. Although the overall fold of Dr RecA is similar to E.coli RecA, there is a large reorientation of the C-terminal domain, which in E.coli RecA has a site for binding dsDNA. Compared to E.coli RecA, the inner surface along the central axis of the Dr RecA filament has an increased positive electrostatic potential. Unique amino acid residues in Dr RecA cluster around a flexible beta-hairpin that has also been implicated in DNA binding.
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Affiliation(s)
- Rakhi Rajan
- Department of Molecular and Cellular Biochemistry, Ohio State University College of Medicine and Public Health, 371 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA
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28
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Xing X, Bell CE. Crystal structures of Escherichia coli RecA in a compressed helical filament. J Mol Biol 2004; 342:1471-85. [PMID: 15364575 DOI: 10.1016/j.jmb.2004.07.091] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Revised: 07/26/2004] [Accepted: 07/27/2004] [Indexed: 11/29/2022]
Abstract
The X-ray crystal structure of uncomplexed Escherichia coli RecA protein has been determined in three new crystal forms at resolutions of 1.9 A, 2.0 A, and 2.6 A. The RecA protein used for this study contains the extra residues Gly-Ser-His-Met at the N terminus, but retains normal ssDNA-dependent ATPase and coprotease activities. In all three crystals, RecA is packed in a right-handed helical filament with a pitch of approximately 74 A. These RecA filaments are compressed relative to the original crystal structure of RecA, which has a helical pitch of 82.7 A. In the structures of the compressed RecA filament, the monomer-monomer interface and the core domain are essentially the same as in the RecA structure with the 83 A pitch. The change in helical pitch is accommodated by a small movement of the N-terminal domain, which is reoriented to preserve the contacts it makes at the monomer-monomer interface. The new crystal structures show significant variation in the orientation and conformation of the C-terminal domain, as well as in the inter-filament packing interactions. In crystal form 2, a calcium ion is bound closely to a beta-hairpin of the C-terminal domain and to Asp38 of a neighboring filament, and residues 329-331 of the C-terminal tail become ordered to contact a neighboring filament. In crystal forms 3 and 4, a sulfate ion or a phosphate anion is bound to the same site on RecA as the beta-phosphate group of ADP, causing an opening of the P-loop. Altogether, the structures show the conformational variability of RecA protein in the crystalline state, providing insight into many aspects of RecA function.
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Affiliation(s)
- Xu Xing
- Department of Molecular and Cellular Biochemistry, Ohio State University College of Medicine and Public Health, 371 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA
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29
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Roca AI, Singleton SF. Direct evaluation of a mechanism for activation of the RecA nucleoprotein filament. J Am Chem Soc 2004; 125:15366-75. [PMID: 14664581 DOI: 10.1021/ja0270165] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RecA protein of Escherichia coli controls the SOS response for DNA damage tolerance and plays a crucial role in recombinational DNA repair. The formation of a RecA.ATP.ssDNA complex initiates all RecA activities, and yet this process is not understood at the molecular level. An analysis of RecA.DNA interactions was performed using both a mutant RecA protein containing a tryptophan (Trp) reporter and oligodeoxyribonucleotides (ODNs) containing a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Experiments using fluorescent ODNs allowed structurally distinct nucleoprotein filaments, formed in the absence and presence of ATPgammaS (a slowly hydrolyzed analogue of ATP), to be differentiated directly. Stopped-flow spectrofluorometry, combined with presteady-state kinetic analyses, revealed unexpected differences in the rates of RecA.ODN and RecA.ATPgammaS.ODN complex assembly. This is the first demonstration that such intrinsically fluorescent synthetic DNAs can be used to characterize definitively the real-time assembly and activation of RecA.ssDNA complexes. Surprisingly, the ssDNA binding event is almost 50-fold slower in the presence of the activating ATPgammaS cofactor. Furthermore, a combination of time-dependent emission changes from 6MI and Trp allowed the first direct chemical test of whether an inactive filament can isomerize to the active state. The results revealed that, unlike the hexameric motor proteins, the inactive RecA filament cannot directly convert to the active state upon ATPgammaS binding. These results have implications for understanding how a coincidence of functions--an ATP-communicated signal-like activity and an ATP-driven motorlike activity--are resolved within a single protein molecule.
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Affiliation(s)
- Alberto I Roca
- Department of Chemistry, Rice University, P.O. Box 1892 MS 65, Houston, TX 77251-1892, USA
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30
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VanLoock MS, Yu X, Yang S, Galkin VE, Huang H, Rajan SS, Anderson WF, Stohl EA, Seifert HS, Egelman EH. Complexes of RecA with LexA and RecX differentiate between active and inactive RecA nucleoprotein filaments. J Mol Biol 2003; 333:345-54. [PMID: 14529621 DOI: 10.1016/j.jmb.2003.08.053] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The bacterial RecA protein has been the dominant model system for understanding homologous genetic recombination. Although a crystal structure of RecA was solved ten years ago, we still do not have a detailed understanding of how the helical filament formed by RecA on DNA catalyzes the recognition of homology and the exchange of strands between two DNA molecules. Recent structural and spectroscopic studies have suggested that subunits in the helical filament formed in the RecA crystal are rotated when compared to the active RecA-ATP-DNA filament. We examine RecA-DNA-ATP filaments complexed with LexA and RecX to shed more light on the active RecA filament. The LexA repressor and RecX, an inhibitor of RecA, both bind within the deep helical groove of the RecA filament. Residues on RecA that interact with LexA cannot be explained by the crystal filament, but can be properly positioned in an existing model for the active filament. We show that the strand exchange activity of RecA, which can be inhibited when RecX is present at very low stoichiometry, is due to RecX forming a block across the deep helical groove of the RecA filament, where strand exchange occurs. It has previously been shown that changes in the nucleotide bound to RecA are associated with large motions of RecA's C-terminal domain. Since RecX binds from the C-terminal domain of one subunit to the nucleotide-binding core of another subunit, a stabilization of RecA's C-terminal domain by RecX can likely explain the inhibition of RecA's ATPase activity by RecX.
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Affiliation(s)
- Margaret S VanLoock
- Department of Biochemistry and Molecular Genetics, University of Virginia Health Sciences Center, Charlottesville, VA 22908-0733, USA
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31
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Xiao J, Singleton SF. Elucidating a key intermediate in homologous DNA strand exchange: structural characterization of the RecA-triple-stranded DNA complex using fluorescence resonance energy transfer. J Mol Biol 2002; 320:529-58. [PMID: 12096908 DOI: 10.1016/s0022-2836(02)00462-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The RecA protein of Escherichia coli plays essential roles in homologous recombination and restarting stalled DNA replication forks. In vitro, the protein mediates DNA strand exchange between single-stranded (ssDNA) and homologous double-stranded DNA (dsDNA) molecules that serves as a model system for the in vivo processes. To date, no high-resolution structure of the key intermediate, comprised of three DNA strands simultaneously bound to a RecA filament (RecA-tsDNA complex), has been reported. We present a systematic characterization of the helical geometries of the three DNA strands of the RecA-tsDNA complex using fluorescence resonance energy transfer (FRET) under physiologically relevant solution conditions. FRET donor and acceptor dyes were used to label different DNA strands, and the interfluorophore distances were inferred from energy transfer efficiencies measured as a function of the base-pair separation between the two dyes. The energy transfer efficiencies were first measured on a control RecA-dsDNA complex, and the calculated helical parameters (h approximately 5 A, Omega(h) approximately 20 degrees ) were consistent with structural conclusions derived from electron microscopy (EM) and other classic biochemical methods. Measurements of the helical parameters for the RecA-tsDNA complex revealed that all three DNA strands adopt extended and unwound conformations similar to those of RecA-bound dsDNA. The structural data are consistent with the hypothesis that this complex is a late, post-strand-exchange intermediate with the outgoing strand shifted by about three base-pairs with respect to its registry with the incoming and complementary strands. Furthermore, the bases of the incoming and complementary strands are displaced away from the helix axis toward the minor groove of the heteroduplex, and the bases of the outgoing strand lie in the major groove of the heteroduplex. We present a model for the strand exchange intermediate in which homologous contacts preceding strand exchange arise in the minor groove of the substrate dsDNA.
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Affiliation(s)
- Jie Xiao
- Department of Chemistry, Rice University, P.O. Box 1892, MS 65, Houston, TX 77005, USA
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32
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Svingen R, Takahashi M, Åkerman B. Gel-Shift Assays: Migrative Dissociation of a RecA−Oligonucleotide Complex during Electrophoresis in Hydroxyethylated Agarose Gels. J Phys Chem B 2001. [DOI: 10.1021/jp011674e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roine Svingen
- Department of Physical Chemistry, Chalmers University of Technology, Göteborg, Sweden, and Department of Biocatalysis, University of Nantes and Centre National de la Recherche Scientifique, Nantes, France
| | - Masayuki Takahashi
- Department of Physical Chemistry, Chalmers University of Technology, Göteborg, Sweden, and Department of Biocatalysis, University of Nantes and Centre National de la Recherche Scientifique, Nantes, France
| | - Björn Åkerman
- Department of Physical Chemistry, Chalmers University of Technology, Göteborg, Sweden, and Department of Biocatalysis, University of Nantes and Centre National de la Recherche Scientifique, Nantes, France
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33
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Berger MD, Lee AM, Simonette RA, Jackson BE, Roca AI, Singleton SF. Design and evaluation of a tryptophanless RecA protein with wild type activity. Biochem Biophys Res Commun 2001; 286:1195-203. [PMID: 11527427 DOI: 10.1006/bbrc.2001.5525] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The C-terminal domain of the Escherichia coli RecA protein contains two tryptophan residues whose native fluorescence emission provides an interfering background signal when other fluorophores such as 1,N(6)-ethenoadenine, 2-aminopurine and other tryptophan residues are used to probe the protein's activities. Replacement of the wild type tryptophans with nonfluorescent residues is not trivial because one tryptophan is highly conserved and the C-terminal domain functions in both DNA binding as well as interfilament protein-protein contact. We undertook the task of creating a tryptophanless RecA protein with WT RecA activity by selecting suitable amino acid replacements for Trp290 and Trp308. Mutant proteins were screened in vivo using assays of SOS induction and cell survival following UV irradiation. Based on its activity in these assays, the W290H-W308F W-less RecA was purified for in vitro characterization and functioned like WT RecA in DNA-dependent ATPase and DNA strand exchange assays. Spectrofluorometry indicates that the W290H-W308F RecA protein generates no significant emission when excited with 295-nm light. Based on its ability to function as wild type protein in vivo and in vitro, this dark RecA protein will be useful for future fluorescence experiments.
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Affiliation(s)
- M D Berger
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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34
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Yu X, Jacobs SA, West SC, Ogawa T, Egelman EH. Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA. Proc Natl Acad Sci U S A 2001; 98:8419-24. [PMID: 11459984 PMCID: PMC37452 DOI: 10.1073/pnas.111005398] [Citation(s) in RCA: 191] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both the bacterial RecA protein and the eukaryotic Rad51 protein form helical nucleoprotein filaments on DNA that catalyze strand transfer between two homologous DNA molecules. However, only the ATP-binding cores of these proteins have been conserved, and this same core is also found within helicases and the F1-ATPase. The C-terminal domain of the RecA protein forms lobes within the helical RecA filament. However, the Rad51 proteins do not have the C-terminal domain found in RecA, but have an N-terminal extension that is absent in the RecA protein. Both the RecA C-terminal domain and the Rad51 N-terminal domain bind DNA. We have used electron microscopy to show that the lobes of the yeast and human Rad51 filaments appear to be formed by N-terminal domains. These lobes are conformationally flexible in both RecA and Rad51. Within RecA filaments, the change between the "active" and "inactive" states appears to mainly involve a large movement of the C-terminal lobe. The N-terminal domain of Rad51 and the C-terminal domain of RecA may have arisen from convergent evolution to play similar roles in the filaments.
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Affiliation(s)
- X Yu
- Department of Biochemistry and Molecular Genetics, University of Virginia Health Sciences Center, Box 800733, Charlottesville, VA 22908, USA
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35
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Kelley De Zutter J, Forget AL, Logan KM, Knight KL. Phe217 regulates the transfer of allosteric information across the subunit interface of the RecA protein filament. Structure 2001; 9:47-55. [PMID: 11342134 DOI: 10.1016/s0969-2126(00)00552-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND ATP-mediated cooperative assembly of a RecA nucleoprotein filament activates the protein for catalysis of DNA strand exchange. RecA is a classic allosterically regulated enzyme in that ATP binding results in a dramatic increase in ssDNA binding affinity. This increase in ssDNA binding affinity results almost exclusively from an ATP-mediated increase in cooperative filament assembly rather than an increase in the inherent affinity of monomeric RecA for DNA. Therefore, certain residues at the subunit interface must play an important role in transmitting allosteric information across the filament structure of RecA. RESULTS Using electron microscopic analysis of RecA polymer formation in the absence of DNA, we show that while wild-type RecA undergoes a slight decrease in filament length in the presence of ATP, a Phe217Tyr substitution results in a dramatic ATP-induced increase in cooperative filament assembly. Biosensor DNA binding measurements reveal that the Phe217Tyr mutation increases ATP-mediated cooperative interaction between RecA subunits by more than 250-fold. CONCLUSIONS These studies represent the first identification of a subunit interface residue in RecA (Phe217) that plays a critical role in regulating the flow of ATP-mediated information throughout the protein filament structure. We propose a model by which conformational changes that occur upon ATP binding are propagated through the structure of a RecA monomer, resulting in the insertion of the Phe217 side chain into a pocket in the neighboring subunit. This event serves as a key step in intersubunit communication leading to ATP-mediated cooperative filament assembly and high affinity binding to ssDNA.
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Affiliation(s)
- J Kelley De Zutter
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
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36
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Eldin S, Forget AL, Lindenmuth DM, Logan KM, Knight KL. Mutations in the N-terminal region of RecA that disrupt the stability of free protein oligomers but not RecA-DNA complexes. J Mol Biol 2000; 299:91-101. [PMID: 10860724 DOI: 10.1006/jmbi.2000.3721] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have introduced targeted mutations in two areas that make up part of the RecA subunit interface. In the RecA crystal structure, cross-subunit interactions are observed between the Lys6 and Asp139 side-chains, and between the Arg28 and Asn113 side-chains. Unexpectedly, we find that mutations at Lys6 and Arg28 impose sever defects on the oligomeric stability of free RecA protein, whereas mutations at Asn113 or Asp139 do not. However, Lys6 and Arg28 mutant proteins showed an apparent normal formation of RecA-DNA complexes. These results suggest that cross-subunit contacts in this region of the protein are different for free RecA protein filaments versus RecA-DNA nucleoprotein filaments. Mutant proteins with substitutions at either Lys6 or Arg28 show partial inhibition of DNA strand exchange activity, yet the mechanistic reasons for this inhibition appear to be distinct. Although Lys6 and Arg28 appear to be more important to the stability of free RecA protein, as opposed to the stability of the catalytically active nucleoprotein filament, our results support the idea that the cross-subunit interactions made by each residue play an important role in optimizing the catalytic organization of the active RecA oligomer.
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Affiliation(s)
- S Eldin
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Medical Center, Worcester, MA 01655-0103, USA
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37
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Gourves AS, Tanguy Le Gac N, Villani G, Boehmer PE, Johnson NP. Equilibrium binding of single-stranded DNA with herpes simplex virus type I-coded single-stranded DNA-binding protein, ICP8. J Biol Chem 2000; 275:10864-9. [PMID: 10753882 DOI: 10.1074/jbc.275.15.10864] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have carried out solution equilibrium binding studies of ICP8, the major single-stranded DNA (ssDNA)-binding protein of herpes simplex virus type I, in order to determine the thermodynamic parameters for its interaction with ssDNA. Fluorescence anisotropy measurements of a 5'-fluorescein-labeled 32-mer oligonucleotide revealed that ICP8 formed a nucleoprotein filament on ssDNA with a binding site size of 10 nucleotides/ICP8 monomer, an association constant at 25 degrees C, K = 0.55 +/- 0.05 x 10(6) M(-1), and a cooperativity parameter, omega = 15 +/- 3. The equilibrium constant was largely independent of salt, deltalog(Komega)/deltalog([NaCl]) = -2.4 +/- 0.4. Comparison of these parameters with other ssDNA-binding proteins showed that ICP8 reacted with an unusual mechanism characterized by low cooperativity and weak binding. In addition, the reaction product was more stable at high salt concentrations, and fluorescence enhancement of etheno-ssDNA by ICP8 was higher than for other ssDNA-binding proteins. These last two characteristics are also found for protein-DNA complexes formed by recombinases in their active conformation. Given the proposed role of ICP8 in promoting strand transfer reactions, they suggest that ICP8 and recombinase proteins may catalyze homologous recombination by a similar mechanism.
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Affiliation(s)
- A S Gourves
- Institut de Pharmacologie et de Biologie Structurale, CNRS, 205 Route de Narbonne, 31077 Toulouse Cédex, France
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38
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Isaev-Ivanov VV, Kozlov MG, Baitin DM, Masui R, Kuramitsu S, Lanzov VA. Fluorescence and excitation Escherichia coli RecA protein spectra analyzed separately for tyrosine and tryptophan residues. Arch Biochem Biophys 2000; 376:124-40. [PMID: 10729198 DOI: 10.1006/abbi.2000.1698] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The method for separation of emission (EM) and excitation (EX) spectra of a protein into EM and EX spectra of its tyrosine (Tyr) and tryptophan (Trp) residues was described. The method was applied to analysis of Escherichia coli RecA protein and its complexes with Mg(2+), ATPgammaS or ADP, and single-stranded DNA (ssDNA). RecA consists of a C-terminal domain containing two Trp and two Tyr residues, a major domain with five Tyr residues, and an N-terminal domain without these residues (R. M. Story, I. T. Weber, and T. A. Steitz (1992) Nature (London) 355, 374-376). Because the fluorescence of Tyr residues in the C-terminal domain was shown to be quenched by energy transfer to Trp residues, Trp and Tyr fluorescence of RecA was provided by the C-terminal and the major domains, respectively. Spectral analysis of Trp and Tyr constituents revealed that a relative spatial location of the C-terminal and the major domains in RecA monomers was different for their complexes with either ATPgammaS or ADP, whereas this location did not change upon additional interaction of these complexes with ssDNA. Homogeneous (that is, independent of EX wavelength) and nonhomogeneous (dependent on EX wavelength) types of Tyr and Trp fluorescence quenching were analyzed for RecA and its complexes with nucleotide cofactors and ssDNA. The former was expected to result from singlet-singlet energy transfer from these residues to adenine of ATPgammaS or ADP. By analogy, the latter was suggested to proceed through energy transfer from high vibrational levels of the excited state of Trp and Tyr residues to the adenine. In this case, for correct calculation of the overlap integral, Trp and Tyr donor emission spectra were substituted by the spectral function of convolution of emission and excitation spectra that resulted in a significant increase of the overlap integral and gave an explanation of the nonhomogeneous quenching of Trp residues in the C-terminal domain.
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Affiliation(s)
- V V Isaev-Ivanov
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, 188350, Russia
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39
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Frank EG, Cheng N, Do CC, Cerritelli ME, Bruck I, Goodman MF, Egelman EH, Woodgate R, Steven AC. Visualization of two binding sites for the Escherichia coli UmuD'(2)C complex (DNA pol V) on RecA-ssDNA filaments. J Mol Biol 2000; 297:585-97. [PMID: 10731413 DOI: 10.1006/jmbi.2000.3591] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The heterotrimeric UmuD'(2)C complex of Escherichia coli has recently been shown to possess intrinsic DNA polymerase activity (DNA pol V) that facilitates error-prone translesion DNA synthesis (SOS mutagenesis). When overexpressed in vivo, UmuD'(2)C also inhibits homologous recombination. In both activities, UmuD'(2)C interacts with RecA nucleoprotein filaments. To examine the biochemical and structural basis of these reactions, we have analyzed the ability of the UmuD'(2)C complex to bind to RecA-ssDNA filaments in vitro. As estimated by a gel retardation assay, binding saturates at a stoichiometry of approximately one complex per two RecA monomers. Visualized by cryo-electron microscopy under these conditions, UmuD'(2)C is seen to bind uniformly along the filaments, such that the complexes are completely submerged in the deep helical groove. This mode of binding would impede access to DNA in a RecA filament, thus explaining the ability of UmuD'(2)C to inhibit homologous recombination. At sub-saturating binding, the distribution of UmuD'(2)C complexes along RecA-ssDNA filaments was characterized by immuno-gold labelling with anti-UmuC antibodies. These data revealed preferential binding at filament ends (most likely, at one end). End-specific binding is consistent with genetic models whereby such binding positions the UmuD'(2)C complex (pol V) appropriately for its role in SOS mutagenesis.
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Affiliation(s)
- E G Frank
- Section on DNA Replication Repair, National Institute of Child Health and Human Development, Bethesda, MD, 20892-2725, USA
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40
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Cox MM. Recombinational DNA repair in bacteria and the RecA protein. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 63:311-66. [PMID: 10506835 DOI: 10.1016/s0079-6603(08)60726-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In bacteria, the major function of homologous genetic recombination is recombinational DNA repair. This is not a process reserved only for rare double-strand breaks caused by ionizing radiation, nor is it limited to situations in which the SOS response has been induced. Recombinational DNA repair in bacteria is closely tied to the cellular replication systems, and it functions to repair damage at stalled replication forks, Studies with a variety of rec mutants, carried out under normal aerobic growth conditions, consistently suggest that at least 10-30% of all replication forks originating at the bacterial origin of replication are halted by DNA damage and must undergo recombinational DNA repair. The actual frequency may be much higher. Recombinational DNA repair is both the most complex and the least understood of bacterial DNA repair processes. When replication forks encounter a DNA lesion or strand break, repair is mediated by an adaptable set of pathways encompassing most of the enzymes involved in DNA metabolism. There are five separate enzymatic processes involved in these repair events: (1) The replication fork assembled at OriC stalls and/or collapses when encountering DNA damage. (2) Recombination enzymes provide a complementary strand for a lesion isolated in a single-strand gap, or reconstruct a branched DNA at the site of a double-strand break. (3) The phi X174-type primosome (or repair primosome) functions in the origin-independent reassembly of the replication fork. (4) The XerCD site-specific recombination system resolves the dimeric chromosomes that are the inevitable by-product of frequent recombination associated with recombinational DNA repair. (5) DNA excision repair and other repair systems eliminate lesions left behind in double-stranded DNA. The RecA protein plays a central role in the recombination phase of the process. Among its many activities, RecA protein is a motor protein, coupling the hydrolysis of ATP to the movement of DNA branches.
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Affiliation(s)
- M M Cox
- Department of Biochemistry, University of Wisconsin-Madison 53706, USA
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41
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Passy SI, Yu X, Li Z, Radding CM, Masson JY, West SC, Egelman EH. Human Dmc1 protein binds DNA as an octameric ring. Proc Natl Acad Sci U S A 1999; 96:10684-8. [PMID: 10485886 PMCID: PMC17943 DOI: 10.1073/pnas.96.19.10684] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial RecA protein has been the most intensively studied enzyme in homologous genetic recombination. The core of RecA is structurally homologous to that of the F1-ATPase and helicases. Like the F1-ATPase and ring helicases, RecA forms a hexameric ring. The human Dmc1 (hDmc1) protein, a meiosis-specific recombinase, is homologous to RecA. We show that hDmc1 forms octameric rings. Unlike RecA and Rad51, however, hDmc1 protein does not form helical filaments. The hDmc1 ring binds DNA in the central channel, as do the ring helicases, which is likely to represent the active form of the protein. These observations indicate that the conservation of the RecA-like ring structure extends from bacteria to humans, and that some RecA homologs may form both rings and filaments, whereas others may function only as rings.
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Affiliation(s)
- S I Passy
- Department of Biology, Rensselaer Polytechnic Institute, 425 Jordan Road, Troy, NY 12180, USA
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42
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Hegner M, Smith SB, Bustamante C. Polymerization and mechanical properties of single RecA-DNA filaments. Proc Natl Acad Sci U S A 1999; 96:10109-14. [PMID: 10468570 PMCID: PMC17850 DOI: 10.1073/pnas.96.18.10109] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The polymerization of individual RecA-DNA filaments, containing either single-stranded or double-stranded DNA, was followed in real time, and their mechanical properties were characterized with force-measuring laser tweezers. It was found that the stretch modulus of a filament is dominated by its (central) DNA component, while its bending rigidity is controlled by its (eccentric) protein component. The longitudinal stiffness of DNA increases 6- to 12-fold when the DNA is contained in the protein helix. Both the stretch modulus and the bending rigidity of a fiber change in the presence of various nucleotide cofactors-e.g., [gamma-thio]ATP, ATP, and ADP-indicating a substantial re-arrangement of spatial relationships between the nucleic acid and the protein scaffold. In particular, when complexed with ATP, a fiber becomes twice as extensible as a [gamma-thio]ATP fiber, suggesting that 32% of the DNA-binding sites have been released in its core. Such release may enable easy rotation of the DNA within the protein helix or slippage of the DNA through the center of the protein helix.
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Affiliation(s)
- M Hegner
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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43
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Yu X, Shibata T, Egelman EH. Identification of a defined epitope on the surface of the active RecA-DNA filament using a monoclonal antibody and three-dimensional reconstruction. J Mol Biol 1998; 283:985-92. [PMID: 9799638 DOI: 10.1006/jmbi.1998.2141] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Studies of the Escherichia coli RecA protein are expected to illuminate mechanisms of DNA recombination and repair in bacteria, and in all higher organisms as well, due to the functional and structural homology with the eukaryotic Rad51 protein. The active form of the RecA protein is a helical filament formed on DNA in the presence of ATP or ATP analogs, and this has been studied at low-resolution by electron microscopy. An atomic model of the protein comes from an X-ray crystallographic study of a filament formed in the absence of DNA and ATP. This filament is believed to be an inactive, storage form of the protein. A key step in generating an atomic model of the active filament, and a detailed model for function, is to understand the large conformational changes that occur between these two states. Towards this end, we have decorated active RecA-DNA filaments with monoclonal antibodies (ARM191) against a known epitope (residues 285 to 320) to determine the position of this epitope in the low-resolution structure. Electron microscopy and three-dimensional reconstruction of the RecA-antibody complex reveal that the lobe containing the epitope is very disordered on the surface of the filament, but in a position similar to that in the inactive crystal filament. The antibody binding also induces a significant conformational change in the RecA filament. This study shows that the basic orientation of the subunit is likely to be similar within the inactive and active filaments, and that the large movement of mass that occurs between these two states must involve other residues than the 285-320 region.
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Affiliation(s)
- X Yu
- Department of Cell Biology and Neuroanatomy, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
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Cazaux C, Blanchet JS, Dupuis D, Villani G, Defais M, Johnson NP. Investigation of the secondary DNA-binding site of the bacterial recombinase RecA. J Biol Chem 1998; 273:28799-804. [PMID: 9786879 DOI: 10.1074/jbc.273.44.28799] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The L2 loop is a DNA-binding site of RecA protein, a recombinase from Eschericha coli. Two DNA-binding sites have been functionally defined in this protein. To determine whether the L2 loop of RecA protein is part of the primary or secondary binding site, we have constructed proteins with site-specific mutations in the loop and investigated their biological, biochemical, and DNA binding properties. The mutation E207Q inhibits DNA repair and homologous recombination in vivo and prevents DNA strand exchange in vitro (Larminat, F., Cazaux, C., Germanier, M., and Defais, M. (1992) J. Bacteriol. 174, 6264-6269; Cazaux, C., Larminat, F., Villani, G., Johnson, N. P., Schnarr, M., and Defais, M. (1994) J. Biol. Chem. 269, 8246-8254). We have found that mutant protein RecAE207Q lacked one of the two single stranded DNA-binding sites of wild type RecA. The remaining site was functional, and biochemical activities of the mutant protein were the same as wild type RecA with ssDNA in the primary binding site. The second mutation, E207K, reduced but did not eliminate DNA repair, SOS induction, and homologous recombination in vivo. In the presence of ATP, mutant protein RecAE207K catalyzed DNA strand exchange in vitro at a slower rate than wild type protein, and ssDNA binding at site I was competitively inhibited. These results show that the L2 loop is or is part of the functional secondary DNA-binding site of RecA protein.
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Affiliation(s)
- C Cazaux
- Institut de Pharmacologie et de Biologie Structurale du CNRS, 205, route de Narbonne, 31077 Toulouse Cedex, France
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Konola JT, Guzzo A, Gow JB, Walker GC, Knight KL. Differential cleavage of LexA and UmuD mediated by recA Pro67 mutants: implications for common LexA and UmuD binding sites on RecA. J Mol Biol 1998; 276:405-15. [PMID: 9512712 DOI: 10.1006/jmbi.1997.1531] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Escherichia coli, RecA-mediated cleavage of LexA repressor is a key regulatory event required for expression of SOS genes involved in the repair of DNA damage. RecA also mediates the cleavage of UmuD protein to UmuD, a form active in SOS mutagenesis. To determine whether LexA and UmuD have common binding determinants on RecA, we have compared the ability of several recA mutants to function in the cleavage of LexA versus UmuD in vivo. The data reveal that while some recA mutations at Pro67 have a similar effect on LexA and UmuD cleavage, others have striking differential effects. For example, a Pro67-->Trp mutation results in a high level of constitutive cleavage of both proteins. However, Pro67-->Asp and Glu mutations promote constitutive cleavage of LexA and reduce induction of UmuD cleavage to just 5 to 10% of wild-type activity. In contrast, Pro67-->Arg prevents LexA cleavage while allowing nearly 50% of wild-type induction of UmuD cleavage. These results are consistent with the idea that Pro67 is located at a site in the nucleoprotein filament where both LexA and UmuD contact RecA.
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Affiliation(s)
- J T Konola
- Department of Biochemistry and Molecular Biology, University of Massachusetts Medical Center, Worcester 01655, USA
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Wittung P, Ellouze C, Maraboeuf F, Takahashi M, Nordèn B. Thermochemical and kinetic evidence for nucleotide-sequence-dependent RecA-DNA interactions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 245:715-9. [PMID: 9183010 DOI: 10.1111/j.1432-1033.1997.00715.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
RecA catalyses homologous recombination in Escherichia coli by promoting pairing of homologous DNA molecules after formation of a helical nucleoprotein filament with single-stranded DNA. The primary reaction of RecA with DNA is generally assumed to be unspecific. We show here, by direct measurement of the interaction enthalpy by means of isothermal titration calorimetry, that the polymerisation of RecA on single-stranded DNA depends on the DNA sequence, with a high exothermic preference for thymine bases. This enthalpic sequence preference of thymines by RecA correlates with faster binding kinetics of RecA to thymine DNA. Furthermore, the enthalpy of interaction between the RecA x DNA filament and a second DNA strand is large only when the added DNA is complementary to the bound DNA in RecA. This result suggests a possibility for a rapid search mechanism by RecA x DNA filaments for homologous DNA molecules.
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Affiliation(s)
- P Wittung
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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Roca AI, Cox MM. RecA protein: structure, function, and role in recombinational DNA repair. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 56:129-223. [PMID: 9187054 DOI: 10.1016/s0079-6603(08)61005-3] [Citation(s) in RCA: 324] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- A I Roca
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin, Madison 53706, USA
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Gardner RV, Voloshin ON, Camerini-Otero RD. The identification of the single-stranded DNA-binding domain of the Escherichia coli RecA protein. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 233:419-25. [PMID: 7588783 DOI: 10.1111/j.1432-1033.1995.419_2.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To identify the ssDNA-binding domain of Escherichia coli RecA protein, we examined the ssDNA-binding capabilities of synthetic peptides, the sequences of which were derived from the C- and N-termini and from sequences within loops L1 and L2 of the RecA molecule identified from the crystal structure. Synthetic peptides derived from amino acid residues 185-219 of several bacterial RecA proteins, which include loop L2 of RecA, bound to ssDNA in filter-binding assays, whereas three separate synthetic peptides corresponding to single point mutants of E. coli RecA in this region did not. The binding of RecA to ssDNA examined using a gel-shift assay was inhibited by a synthetic peptide derived from this ssDNA-binding region, but not by synthetic peptides derived from amino acid residues 301-329 of the C-terminus or from N-terminal residues 6-39. A peptide corresponding to amino acid positions 152-169 of the RecA molecule and spanning loop L1 and its flanking regions did not bind ssDNA at peptide concentrations up to 250 microM. We have also defined a synthetic 20-amino-acid peptide that comprises amino acid residues 193-212 and includes loop L2 of RecA as the minimum unit that can bind to ssDNA from this region of RecA. Finally, two maltose-binding protein-RecA fusion proteins were made, one containing amino acid residues 185-224 of RecA and the other the last 51 C-terminal residues of RecA (amino acid residues 303-353). In contrast to the C-terminus-derived fusion protein, the fusion protein containing the putative DNA-binding site demonstrated significant binding to single-stranded oligonucleotides in both filter-binding and gel-shift assays. These findings suggest that a portion of the region extending from amino acid residues 193-212 is either part of or the whole ssDNA-binding domain of the RecA protein.
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Affiliation(s)
- R V Gardner
- Genetics and Biochemistry Branch, National Institutes of Health, Bethesda, Maryland 20892-1810, USA
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Morimatsu K, Horii T. The DNA-Binding Site of the Reca Protein. Photochemical Cross-Linking of Tyrl03 to Single-Stranded DNA. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.tb20322.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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West SC. Formation, translocation and resolution of Holliday junctions during homologous genetic recombination. Philos Trans R Soc Lond B Biol Sci 1995; 347:21-5. [PMID: 7746849 DOI: 10.1098/rstb.1995.0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Over the past three or four years, great strides have been made in our understanding of the proteins involved in recombination and the mechanisms by which recombinant molecules are formed. This review summarizes our current understanding of the process by focusing on recent studies of proteins involved in the later steps of recombination in bacteria. In particular, biochemical investigation of the in vitro properties of the E. coli RuvA, RuvB and RuvC proteins have provided our first insight into the novel insight into the novel molecular mechanisms by which Holliday junctions are moved along DNA and then resolved by endonucleolytic cleavage.
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Affiliation(s)
- S C West
- Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Herts, U.K
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