1
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Knadler C, Graham V W, Rolfsmeier M, Haseltine CA. Divalent metal cofactors differentially modulate RadA-mediated strand invasion and exchange in Saccharolobus solfataricus. Biosci Rep 2023; 43:BSR20221807. [PMID: 36601994 PMCID: PMC9950535 DOI: 10.1042/bsr20221807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Central to the universal process of recombination, RecA family proteins form nucleoprotein filaments to catalyze production of heteroduplex DNA between substrate ssDNAs and template dsDNAs. ATP binding assists the filament in assuming the necessary conformation for forming heteroduplex DNA, but hydrolysis is not required. ATP hydrolysis has two identified roles which are not universally conserved: promotion of filament dissociation and enhancing flexibility of the filament. In this work, we examine ATP utilization of the RecA family recombinase SsoRadA from Saccharolobus solfataricus to determine its function in recombinase-mediated heteroduplex DNA formation. Wild-type SsoRadA protein and two ATPase mutant proteins were evaluated for the effects of three divalent metal cofactors. We found that unlike other archaeal RadA proteins, SsoRadA-mediated strand exchange is not enhanced by Ca2+. Instead, the S. solfataricus recombinase can utilize Mn2+ to stimulate strand invasion and reduce ADP-binding stability. Additionally, reduction of SsoRadA ATPase activity by Walker Box mutation or cofactor alteration resulted in a loss of large, complete strand exchange products. Depletion of ADP was found to improve initial strand invasion but also led to a similar loss of large strand exchange events. Our results indicate that overall, SsoRadA is distinct in its use of divalent cofactors but its activity with Mn2+ shows similarity to human RAD51 protein with Ca2+.
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Affiliation(s)
- Corey J. Knadler
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - William J. Graham V
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Michael L. Rolfsmeier
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Cynthia A. Haseltine
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
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2
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Peter B, Falkenberg M. TWINKLE and Other Human Mitochondrial DNA Helicases: Structure, Function and Disease. Genes (Basel) 2020; 11:genes11040408. [PMID: 32283748 PMCID: PMC7231222 DOI: 10.3390/genes11040408] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/30/2022] Open
Abstract
Mammalian mitochondria contain a circular genome (mtDNA) which encodes subunits of the oxidative phosphorylation machinery. The replication and maintenance of mtDNA is carried out by a set of nuclear-encoded factors—of which, helicases form an important group. The TWINKLE helicase is the main helicase in mitochondria and is the only helicase required for mtDNA replication. Mutations in TWINKLE cause a number of human disorders associated with mitochondrial dysfunction, neurodegeneration and premature ageing. In addition, a number of other helicases with a putative role in mitochondria have been identified. In this review, we discuss our current knowledge of TWINKLE structure and function and its role in diseases of mtDNA maintenance. We also briefly discuss other potential mitochondrial helicases and postulate on their role(s) in mitochondria.
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3
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Peter B, Farge G, Pardo-Hernandez C, Tångefjord S, Falkenberg M. Structural basis for adPEO-causing mutations in the mitochondrial TWINKLE helicase. Hum Mol Genet 2019; 28:1090-1099. [PMID: 30496414 PMCID: PMC6423418 DOI: 10.1093/hmg/ddy415] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022] Open
Abstract
TWINKLE is the helicase involved in replication and maintenance of mitochondrial DNA (mtDNA) in mammalian cells. Structurally, TWINKLE is closely related to the bacteriophage T7 gp4 protein and comprises a helicase and primase domain joined by a flexible linker region. Mutations in and around this linker region are responsible for autosomal dominant progressive external ophthalmoplegia (adPEO), a neuromuscular disorder associated with deletions in mtDNA. The underlying molecular basis of adPEO-causing mutations remains unclear, but defects in TWINKLE oligomerization are thought to play a major role. In this study, we have characterized these disease variants by single-particle electron microscopy and can link the diminished activities of the TWINKLE variants to altered oligomeric properties. Our results suggest that the mutations can be divided into those that (i) destroy the flexibility of the linker region, (ii) inhibit ring closure and (iii) change the number of subunits within a helicase ring. Furthermore, we demonstrate that wild-type TWINKLE undergoes large-scale conformational changes upon nucleoside triphosphate binding and that this ability is lost in the disease-causing variants. This represents a substantial advancement in the understanding of the molecular basis of adPEO and related pathologies and may aid in the development of future therapeutic strategies.
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Affiliation(s)
- Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Sweden
| | - Geraldine Farge
- Centre Nacionale de la Recherche Scientifique/Institut National de Physique Nucléaire et des Particules, Laboratoire de Physique de Clermont, Université Clermont Auvergne, BP 10448, Clermont-Ferrand, France
| | | | - Stefan Tångefjord
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Sweden
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4
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Patoli BB, Winter JA, Patoli AA, Delahay RM, Bunting KA. Co-expression and purification of the RadA recombinase with the RadB paralog from Haloferax volcanii yields heteromeric ring-like structures. Microbiology (Reading) 2017; 163:1802-1811. [DOI: 10.1099/mic.0.000562] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bushra B. Patoli
- School of Biology, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
- Present address: Institute of Microbiology, University of Sindh, Jamshoro, Pakistan
| | - Jody A. Winter
- School of Biology, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
- Present address: Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Atif A. Patoli
- School of Biology, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
- Present address: Institute of Microbiology, University of Sindh, Jamshoro, Pakistan
| | - Robin M. Delahay
- School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Karen A. Bunting
- School of Biology, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
- Present address: Albumedix Ltd, Nottingham, NG7 1FD, UK
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5
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Korolev S. Advances in structural studies of recombination mediator proteins. Biophys Chem 2016; 225:27-37. [PMID: 27974172 DOI: 10.1016/j.bpc.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 12/25/2022]
Abstract
Recombination mediator proteins (RMPs) are critical for genome integrity in all organisms. They include phage UvsY, prokaryotic RecF, -O, -R (RecFOR) and eukaryotic Rad52, Breast Cancer susceptibility 2 (BRCA2) and Partner and localizer of BRCA2 (PALB2) proteins. BRCA2 and PALB2 are tumor suppressors implicated in cancer. RMPs regulate binding of RecA-like recombinases to sites of DNA damage to initiate the most efficient non-mutagenic repair of broken chromosome and other deleterious DNA lesions. Mechanistically, RMPs stimulate a single-stranded DNA (ssDNA) hand-off from ssDNA binding proteins (ssbs) such as gp32, SSB and RPA, to recombinases, activating DNA repair only at the time and site of the damage event. This review summarizes structural studies of RMPs and their implications for understanding mechanism and function. Comparative analysis of RMPs is complicated due to their convergent evolution. In contrast to the evolutionary conserved ssbs and recombinases, RMPs are extremely diverse in sequence and structure. Structural studies are particularly important in such cases to reveal common features of the entire family and specific features of regulatory mechanisms for each member. All RMPs are characterized by specific DNA-binding domains and include variable protein interaction motifs. The complexity of such RMPs corresponds to the ever-growing number of DNA metabolism events they participate in under normal and pathological conditions and requires additional comprehensive structure-functional studies.
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Affiliation(s)
- S Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 S Grand Blvd., St. Louis, MO 63104, USA.
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6
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Perkins RJ, Kukharchuk A, Delcroix P, Shoemaker RK, Roeselová M, Cwiklik L, Vaida V. The Partitioning of Small Aromatic Molecules to Air–Water and Phospholipid Interfaces Mediated by Non-Hydrophobic Interactions. J Phys Chem B 2016; 120:7408-22. [DOI: 10.1021/acs.jpcb.6b05084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Russell J. Perkins
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, Colorado 80309, United States
- Cooperative
Institute for Research In Environmental Sciences, University of Colorado Boulder, UCV 215, Boulder, Colorado 80309, United States
| | - Alexandra Kukharchuk
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Pauline Delcroix
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Richard K. Shoemaker
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, Colorado 80309, United States
| | - Martina Roeselová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Lukasz Cwiklik
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Veronica Vaida
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, Colorado 80309, United States
- Cooperative
Institute for Research In Environmental Sciences, University of Colorado Boulder, UCV 215, Boulder, Colorado 80309, United States
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7
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Topilina NI, Novikova O, Stanger M, Banavali NK, Belfort M. Post-translational environmental switch of RadA activity by extein-intein interactions in protein splicing. Nucleic Acids Res 2015; 43:6631-48. [PMID: 26101259 PMCID: PMC4513877 DOI: 10.1093/nar/gkv612] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/29/2015] [Indexed: 11/14/2022] Open
Abstract
Post-translational control based on an environmentally sensitive intervening intein sequence is described. Inteins are invasive genetic elements that self-splice at the protein level from the flanking host protein, the exteins. Here we show in Escherichia coli and in vitro that splicing of the RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. High temperature or solution conditions can unlock the intein for full activity, as can remote extein point mutations. Notably, this splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide a novel means of post-translational control.
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Affiliation(s)
- Natalya I Topilina
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Matthew Stanger
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Nilesh K Banavali
- Laboratory of Computational and Structural Biology, Division of Genetics, Wadsworth Center, NYS Department of Health and Department of Biomedical Sciences, University at Albany, CMS 2008, Biggs Lab, Empire State Plaza, PO Box 509, Albany, NY 12201-2002, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
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8
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Han W, Shen Y, She Q. Nanobiomotors of archaeal DNA repair machineries: current research status and application potential. Cell Biosci 2014; 4:32. [PMID: 24995126 PMCID: PMC4080772 DOI: 10.1186/2045-3701-4-32] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 06/13/2014] [Indexed: 11/10/2022] Open
Abstract
Nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. These proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Several archaeal nucleic acid nanobiomotors, such as DNA helicases that unwind double-stranded DNA molecules during DNA damage repair, have been characterized in details. XPB, XPD and Hjm are SF2 family helicases, each of which employs two ATPase domains for ATP binding and hydrolysis to drive DNA unwinding. They also carry additional specific domains for substrate binding and regulation. Another helicase, HerA, forms a hexameric ring that may act as a DNA-pumping enzyme at the end processing of double-stranded DNA breaks. Common for all these nanobiomotors is that they contain ATPase domain that adopts RecA fold structure. This structure is characteristic for RecA/RadA family proteins and has been studied in great details. Here we review the structural analyses of these archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion. The application potential of archaeal nanobiomotors in drug delivery has been discussed.
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Affiliation(s)
- Wenyuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China ; Archaeal Centre, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Copenhagen, Denmark
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| | - Qunxin She
- Archaeal Centre, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Copenhagen, Denmark
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9
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Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:206735. [PMID: 24701133 PMCID: PMC3950489 DOI: 10.1155/2014/206735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/27/2013] [Accepted: 11/29/2013] [Indexed: 12/28/2022]
Abstract
As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
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10
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Du L, Luo Y. Structure of a filament of stacked octamers of human DMC1 recombinase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:382-6. [PMID: 23545642 PMCID: PMC3614161 DOI: 10.1107/s1744309113005678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/26/2013] [Indexed: 11/10/2022]
Abstract
Eukaryal DMC1 proteins play a central role in homologous recombination in meiosis by assembling at the sites of programmed DNA double-strand breaks and carrying out a search for allelic DNA sequences located on homologous chromatids. They are close homologs of eukaryal Rad51 and archaeal RadA proteins and are remote homologs of bacterial RecA proteins. These recombinases (also called DNA strand-exchange proteins) promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. An octameric form of a truncated human DMC1 devoid of its small N-terminal domain (residues 1-83) has been crystallized. The structure of the truncated DMC1 octamer is similar to that of the previously reported full-length DMC1 octamer, which has disordered N-terminal domains. In each protomer, only the ATP cap regions (Asp317-Glu323) show a noticeable conformational difference. The truncated DMC1 octamers further stack with alternate polarity into a filament. Similar filamentous assemblies of DMC1 have been observed to form on DNA by electron microscopy.
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Affiliation(s)
- Liqin Du
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
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11
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Su ZY, Lee WJ, Su WS, Wang YT. Target molecular simulations of RecA family protein filaments. Int J Mol Sci 2012; 13:7138-7148. [PMID: 22837683 PMCID: PMC3397515 DOI: 10.3390/ijms13067138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/10/2012] [Accepted: 05/29/2012] [Indexed: 11/16/2022] Open
Abstract
Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon. We find 11 rotary residues (R72, T75-K81, M84, V86 and K87) and five zero rotary residues (I71, K74, E82, R83 and K88) in the simulations. Inclusion of our simulations may help to understand the RadA family mechanism.
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Affiliation(s)
- Zhi-Yuan Su
- Department of Information Management, Chia Nan University of Pharmacy & Science, No. 60, Sec. 1, Erren Rd., Rende Dist., Tainan City 71710, Taiwan; E-Mail:
| | - Wen-Jay Lee
- National Center for High-Performance Computing, Hsin-Shi, No. 28, Nan-Ke 3rd Rd., Hsin-Shi Dist., Tainan City 74147, Taiwan; E-Mails: (W.-J.L.); (W.-S.S.)
| | - Wan-Sheng Su
- National Center for High-Performance Computing, Hsin-Shi, No. 28, Nan-Ke 3rd Rd., Hsin-Shi Dist., Tainan City 74147, Taiwan; E-Mails: (W.-J.L.); (W.-S.S.)
- Department of Physics, National Chung Hsing University, No. 250, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Yeng-Tseng Wang
- National Center for High-Performance Computing, Hsin-Shi, No. 28, Nan-Ke 3rd Rd., Hsin-Shi Dist., Tainan City 74147, Taiwan; E-Mails: (W.-J.L.); (W.-S.S.)
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12
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Du L, Luo Y. Structure of a hexameric form of RadA recombinase from Methanococcus voltae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:511-6. [PMID: 22691778 PMCID: PMC3374503 DOI: 10.1107/s1744309112010226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 03/07/2012] [Indexed: 11/27/2022]
Abstract
Archaeal RadA proteins are close homologues of eukaryal Rad51 and DMC1 proteins and are remote homologues of bacterial RecA proteins. For the repair of double-stranded breaks in DNA, these recombinases promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. This DNA-repair function also plays a key role in the resistance of cancer cells to chemotherapy and radiotherapy and in the resistance of bacterial cells to antibiotics. A hexameric form of a truncated Methanococcus voltae RadA protein devoid of its small N-terminal domain has been crystallized. The RadA hexamers further assemble into two-ringed assemblies. Similar assemblies can be observed in the crystals of Pyrococcus furiosus RadA and Homo sapiens DMC1. In all of these two-ringed assemblies the DNA-interacting L1 region of each protomer points inward towards the centre, creating a highly positively charged locus. The electrostatic characteristics of the central channels can be utilized in the design of novel recombinase inhibitors.
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Affiliation(s)
- Liqin Du
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
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Etedali F, Baghban Kohnehrouz B, Valizadeh M, Gholizadeh A, Malboobi MA. Genome wide cloning of maize meiotic recombinase Dmc1 and its functional structure through molecular phylogeny. GENETICS AND MOLECULAR RESEARCH 2012; 10:1636-49. [PMID: 21863556 DOI: 10.4238/vol10-3gmr1338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The development of meiotic division and associated genetic recombination paved the way for evolutionary changes. However, the secondary and tertiary structure and functional domains of many of the proteins involved in genetic recombination have not been studied in detail. We used the human Dmc1 gene product along with secondary and tertiary domain structures of Escherichia coli RecA protein to help determine the molecular structure and function of maize Dmc1, which is required for synaptonemal complex formation and cell cycle progression. The maize recombinase Dmc1 gene was cloned and characterized, using rice Dmc1 cDNA as an orthologue. The deduced amino acid sequence was used for elaborating its 3-D structure, and functional analysis was made with the CDD software, showing significant identity of the Dmc1 gene product in Zea mays with that of Homo sapiens. Based on these results, the domains and motives of WalkerA and WalkerB as ATP binding sites, a multimer site (BRC) interface, the putative ssDNA binding L1 and L2 loops, the putative dsDNA binding helix-hairpin-helix, a polymerization motif, the subunit rotation motif, and a small N-terminal domain were proposed for maize recombinase Dmc1.
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Affiliation(s)
- F Etedali
- Department of Plant Breeding and Biotechnology, University of Tabriz, Iran
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14
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Rolfsmeier ML, Laughery MF, Haseltine CA. Repair of DNA Double-Strand Breaks Induced by Ionizing Radiation Damage Correlates with Upregulation of Homologous Recombination Genes in Sulfolobus solfataricus. J Mol Biol 2011; 414:485-98. [DOI: 10.1016/j.jmb.2011.10.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/05/2011] [Accepted: 10/12/2011] [Indexed: 10/16/2022]
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15
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Repair of DNA double-strand breaks following UV damage in three Sulfolobus solfataricus strains. J Bacteriol 2010; 192:4954-62. [PMID: 20675475 DOI: 10.1128/jb.00667-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA damage repair mechanisms have been most thoroughly explored in the eubacterial and eukaryotic branches of life. The methods by which members of the archaeal branch repair DNA are significantly less well understood but have been gaining increasing attention. In particular, the approaches employed by hyperthermophilic archaea have been a general source of interest, since these organisms thrive under conditions that likely lead to constant chromosomal damage. In this work we have characterized the responses of three Sulfolobus solfataricus strains to UV-C irradiation, which often results in double-strand break formation. We examined S. solfataricus strain P2 obtained from two different sources and S. solfataricus strain 98/2, a popular strain for site-directed mutation by homologous recombination. Cellular recovery, as determined by survival curves and the ability to return to growth after irradiation, was found to be strain specific and differed depending on the dose applied. Chromosomal damage was directly visualized using pulsed-field gel electrophoresis and demonstrated repair rate variations among the strains following UV-C irradiation-induced double-strand breaks. Several genes involved in double-strand break repair were found to be significantly upregulated after UV-C irradiation. Transcript abundance levels and temporal expression patterns for double-strand break repair genes were also distinct for each strain, indicating that these Sulfolobus solfataricus strains have differential responses to UV-C-induced DNA double-strand break damage.
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16
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McRobbie AM, Carter LG, Kerou M, Liu H, McMahon SA, Johnson KA, Oke M, Naismith JH, White MF. Structural and functional characterisation of a conserved archaeal RadA paralog with antirecombinase activity. J Mol Biol 2009; 389:661-73. [PMID: 19414020 DOI: 10.1016/j.jmb.2009.04.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 04/20/2009] [Accepted: 04/27/2009] [Indexed: 12/25/2022]
Abstract
DNA recombinases (RecA in bacteria, Rad51 in eukarya and RadA in archaea) catalyse strand exchange between homologous DNA molecules, the central reaction of homologous recombination, and are among the most conserved DNA repair proteins known. RecA is the sole protein responsible for this reaction in bacteria, whereas there are several Rad51 paralogs that cooperate to catalyse strand exchange in eukaryotes. All archaea have at least one (and as many as four) RadA paralog, but their function remains unclear. Herein, we show that the three RadA paralogs encoded by the Sulfolobus solfataricus genome are expressed under normal growth conditions and are not UV inducible. We demonstrate that one of these proteins, Sso2452, which is representative of the large archaeal RadC subfamily of archaeal RadA paralogs, functions as an ATPase that binds tightly to single-stranded DNA. However, Sso2452 is not an active recombinase in vitro and inhibits D-loop formation by RadA. We present the high-resolution crystal structure of Sso2452, which reveals key structural differences from the canonical RecA family recombinases that may explain its functional properties. The possible roles of the archaeal RadA paralogs in vivo are discussed.
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Affiliation(s)
- Anne-Marie McRobbie
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
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17
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Chang YW, Ko TP, Lee CD, Chang YC, Lin KA, Chang CS, Wang AHJ, Wang TF. Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity. PLoS One 2009; 4:e4890. [PMID: 19295907 PMCID: PMC2654063 DOI: 10.1371/journal.pone.0004890] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 02/19/2009] [Indexed: 12/02/2022] Open
Abstract
RecA family proteins, including bacterial RecA, archaeal RadA, and eukaryotic Dmc1 and Rad51, mediate homologous recombination, a reaction essential for maintaining genome integrity. In the presence of ATP, these proteins bind a single-strand DNA to form a right-handed nucleoprotein filament, which catalyzes pairing and strand exchange with a homologous double-stranded DNA (dsDNA), by as-yet unknown mechanisms. We recently reported a structure of RadA left-handed helical filament, and here present three new structures of RadA left-handed helical filaments. Comparative structural analysis between different RadA/Rad51 helical filaments reveals that the N-terminal domain (NTD) of RadA/Rad51, implicated in dsDNA binding, is highly flexible. We identify a hinge region between NTD and polymerization motif as responsible for rigid body movement of NTD. Mutant analysis further confirms that structural flexibility of NTD is essential for RadA's recombinase activity. These results support our previous hypothesis that ATP-dependent axial rotation of RadA nucleoprotein helical filament promotes homologous recombination.
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Affiliation(s)
- Yu-Wei Chang
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chien-Der Lee
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Kuei-Ann Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Andrew H.-J. Wang
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail: (AHJW); (TFW)
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail: (AHJW); (TFW)
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18
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Sandhu KS. Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins. J Mol Recognit 2009; 22:1-8. [PMID: 18802931 DOI: 10.1002/jmr.915] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatin remodelers, a group of proteins involved in nucleosome re-positioning and modification, have extensive range of interacting partners. They form multimeric complexes and interact with modified histones, transcription, splicing, and replication factors, DNA, RNA, and the factors related to the maintenance of chromosome structure. Such diverse range of interactions is hard to explain with the presumed highly structured form of the protein. In the current analysis, the conformations of chromatin remodelers were explored using protein disorder prediction algorithms. The study revealed that a significant proportion (p < 2.2e-16) of these proteins harbor at least one long region of intrinsic disorder (>70 aa). These unstructured regions do not exhibit any preference to the N/C terminal or middle of the protein. They do not show any significant representation in the Protein Data Bank (PDB) structure repository. Limited examples from PDB indicate direct involvement of disordered regions in binding of chromatin remodeling proteins to naked or modified DNA, histones, and other chromatin-related factors. Furthermore, intrinsic disorder seen in these proteins correlates to the presence of low sequence complexity regions (p = 1.851e-10) particularly the tandem repeats of hydrophilic and charged amino acids. This probably hints at their evolutionary origin via repeat expansion. The disordered regions may enable these proteins to reversibly bind to various interacting partners and eventually contribute to functional diversity and specialization of chromatin remodeling complexes. These could also endow combinatorial action of multiple domains within a protein. We further discuss the prominent association of intrinsic disorder with other chromatin-related proteins and its functional relevance therein.
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Affiliation(s)
- Kuljeet Singh Sandhu
- Department of Animal Development and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvagen 18A, Uppsala 75236, Sweden.
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19
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Abstract
Recombinases of the RecA family are essential for homologous recombination and underpin genome stability, by promoting the repair of double-stranded DNA breaks and the rescue of collapsed DNA replication forks. Until now, our understanding of homologous recombination has relied on studies of bacterial and eukaryotic model organisms. Archaea provide new opportunities to study how recombination operates in a lineage distinct from bacteria and eukaryotes. In the present paper, we focus on RadA, the archaeal RecA family recombinase, and its homologues in archaea and other domains. On the basis of phylogenetic analysis, we propose that a family of archaeal proteins with a single RecA domain, which are currently annotated as KaiC, be renamed aRadC.
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20
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Grigorescu AA, Vissers JHA, Ristic D, Pigli YZ, Lynch TW, Wyman C, Rice PA. Inter-subunit interactions that coordinate Rad51's activities. Nucleic Acids Res 2008; 37:557-67. [PMID: 19066203 PMCID: PMC2632893 DOI: 10.1093/nar/gkn973] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rad51 is the central catalyst of homologous recombination in eukaryotes and is thus critical for maintaining genomic integrity. Recent crystal structures of filaments formed by Rad51 and the closely related archeal RadA and eubacterial RecA proteins place the ATPase site at the protomeric interface. To test the relevance of this feature, we mutated conserved residues at this interface and examined their effects on key activities of Rad51: ssDNA-stimulated ATP hydrolysis, DNA binding, polymerization on DNA substrates and catalysis of strand-exchange reactions. Our results show that the interface seen in the crystal structures is very important for nucleoprotein filament formation. H352 and R357 of yeast Rad51 are essential for assembling the catalytically competent form of the enzyme on DNA substrates and coordinating its activities. However, contrary to some previous suggestions, neither of these residues is critical for ATP hydrolysis.
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Affiliation(s)
- Arabela A Grigorescu
- Department of Biochemistry, Molecular Biology and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
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21
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Wang TF, Chen LT, Wang AHJ. Right or left turn? RecA family protein filaments promote homologous recombination through clockwise axial rotation. Bioessays 2008; 30:48-56. [PMID: 18081011 DOI: 10.1002/bies.20694] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The RecA family proteins mediate homologous recombination, a ubiquitous mechanism for repairing DNA double-strand breaks (DSBs) and stalled replication forks. Members of this family include bacterial RecA, archaeal RadA and Rad51, and eukaryotic Rad51 and Dmc1. These proteins bind to single-stranded DNA at a DSB site to form a presynaptic nucleoprotein filament, align this presynaptic filament with homologous sequences in another double-stranded DNA segment, promote DNA strand exchange and then dissociate. It was generally accepted that RecA family proteins function throughout their catalytic cycles as right-handed helical filaments with six protomers per helical turn. However, we recently reported that archaeal RadA proteins can also form an extended right-handed filament with three monomers per helical turn and a left-handed protein filament with four monomers per helical turn. Subsequent structural and functional analyses suggest that RecA family protein filaments, similar to the F1-ATPase rotary motor, perform ATP-dependent clockwise axial rotation during their catalytic cycles. This new hypothesis has opened a new avenue for understanding the molecular mechanism of RecA family proteins in homologous recombination.
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Affiliation(s)
- Ting-Fang Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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22
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Richards JD, Johnson KA, Liu H, McRobbie AM, McMahon S, Oke M, Carter L, Naismith JH, White MF. Structure of the DNA repair helicase hel308 reveals DNA binding and autoinhibitory domains. J Biol Chem 2007; 283:5118-26. [PMID: 18056710 DOI: 10.1074/jbc.m707548200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hel308 is a superfamily 2 helicase conserved in eukaryotes and archaea. It is thought to function in the early stages of recombination following replication fork arrest and has a specificity for removal of the lagging strand in model replication forks. A homologous helicase constitutes the N-terminal domain of human DNA polymerase Q. The Drosophila homologue mus301 is implicated in double strand break repair and meiotic recombination. We have solved the high resolution crystal structure of Hel308 from the crenarchaeon Sulfolobus solfataricus, revealing a five-domain structure with a central pore lined with essential DNA binding residues. The fifth domain is shown to act as an autoinhibitory domain or molecular brake, clamping the single-stranded DNA extruded through the central pore of the helicase structure to limit the helicase activity of the enzyme. This provides an elegant mechanism to tune the processivity of the enzyme to its functional role. Hel308 can displace streptavidin from a biotinylated DNA molecule, and this activity is only partially inhibited when the DNA is pre-bound with abundant DNA-binding proteins RPA or Alba1, whereas pre-binding with the recombinase RadA has no effect on activity. These data suggest that one function of the enzyme may be in the removal of bound proteins at stalled replication forks and recombination intermediates.
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Affiliation(s)
- Jodi D Richards
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, Scotland
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23
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Abella M, Rodríguez S, Paytubi S, Campoy S, White MF, Barbé J. The Sulfolobus solfataricus radA paralogue sso0777 is DNA damage inducible and positively regulated by the Sta1 protein. Nucleic Acids Res 2007; 35:6788-97. [PMID: 17921500 PMCID: PMC2175319 DOI: 10.1093/nar/gkm782] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Little is known about the regulation of the DNA damage-mediated gene expression in archaea. Here we report that the addition of actinomycin D to Sulfolobus solfataricus cultures triggers the expression of the radA paralogue sso0777. Furthermore, a specific retarded band is observed when electrophoretic mobility shift assays (EMSAs) with crude S. solfataricus cell extracts and the sso0777 promoter were carried out. The protein that binds to this promoter was isolated and identified as Sta1. Footprinting experiments have shown that the Sta1 DNA-binding site is included in the ATTTTTTATTTTCACATGTAAGATGTTTATT sequence, which is located upstream the putative TTG translation starting codon of the sso0777 gene. Additionally, gel electrophoretic mobility retardation experiments using mutant sso0777 promoter derivatives show the presence of three essential motifs (TTATT, CANGNA and TTATT) that are absolutely required for Sta1 DNA binding. Finally, in vitro transcription experiments confirm that Sta1 functions as an activator for sso0777 gene expression being the first identified archaeal regulatory protein associated with the DNA damage-mediated induction of gene expression.
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Affiliation(s)
- Marc Abella
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain
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24
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Chen LT, Ko TP, Chang YW, Lin KA, Wang AHJ, Wang TF. Structural and functional analyses of five conserved positively charged residues in the L1 and N-terminal DNA binding motifs of archaeal RADA protein. PLoS One 2007; 2:e858. [PMID: 17848989 PMCID: PMC1964548 DOI: 10.1371/journal.pone.0000858] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Accepted: 08/16/2007] [Indexed: 12/29/2022] Open
Abstract
RecA family proteins engage in an ATP-dependent DNA strand exchange reaction that includes a ssDNA nucleoprotein helical filament and a homologous dsDNA sequence. In spite of more than 20 years of efforts, the molecular mechanism of homology pairing and strand exchange is still not fully understood. Here we report a crystal structure of Sulfolobus solfataricus RadA overwound right-handed filament with three monomers per helical pitch. This structure reveals conformational details of the first ssDNA binding disordered loop (denoted L1 motif) and the dsDNA binding N-terminal domain (NTD). L1 and NTD together form an outwardly open palm structure on the outer surface of the helical filament. Inside this palm structure, five conserved basic amino acid residues (K27, K60, R117, R223 and R229) surround a 25 A pocket that is wide enough to accommodate anionic ssDNA, dsDNA or both. Biochemical analyses demonstrate that these five positively charged residues are essential for DNA binding and for RadA-catalyzed D-loop formation. We suggest that the overwound right-handed RadA filament represents a functional conformation in the homology search and pairing reaction. A new structural model is proposed for the homologous interactions between a RadA-ssDNA nucleoprotein filament and its dsDNA target.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Wei Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuei-An Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Life Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- National Core Facility of High-Throughput Protein Crystallography, Academia Sinica, Taipei, Taiwan
- * To whom correspondence should be addressed. E-mail: (AW); (TW)
| | - Ting-Fang Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * To whom correspondence should be addressed. E-mail: (AW); (TW)
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25
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Chen LT, Ko TP, Chang YC, Lin KA, Chang CS, Wang AHJ, Wang TF. Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins. Nucleic Acids Res 2007; 35:1787-801. [PMID: 17329376 PMCID: PMC1874592 DOI: 10.1093/nar/gkl1131] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RecA family of proteins mediates homologous recombination, an evolutionarily conserved pathway that maintains genomic stability by protecting against DNA double strand breaks. RecA proteins are thought to facilitate DNA strand exchange reactions as closed-rings or as right-handed helical filaments. Here, we report the crystal structure of a left-handed Sulfolobus solfataricus RadA helical filament. Each protomer in this left-handed filament is linked to its neighbour via interactions of a β-strand polymerization motif with the neighbouring ATPase domain. Immediately following the polymerization motif, we identified an evolutionarily conserved hinge region (a subunit rotation motif) in which a 360° clockwise axial rotation accompanies stepwise structural transitions from a closed ring to the AMP–PNP right-handed filament, then to an overwound right-handed filament and finally to the left-handed filament. Additional structural and functional analyses of wild-type and mutant proteins confirmed that the subunit rotation motif is crucial for enzymatic functions of RecA family proteins. These observations support the hypothesis that RecA family protein filaments may function as rotary motors.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Yuan-Chih Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Kuei-An Lin
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Seng Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Ting-Fang Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
- *To whom correspondence should be addressed. +886-2-27855696+886-2-27889759
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26
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Ishino Y, Nishino T, Morikawa K. Mechanisms of maintaining genetic stability by homologous recombination. Chem Rev 2006; 106:324-39. [PMID: 16464008 DOI: 10.1021/cr0404803] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yoshizumi Ishino
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukukoka-shi, Fukuoka, Japan.
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27
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Kojic M, Zhou Q, Lisby M, Holloman WK. Rec2 interplay with both Brh2 and Rad51 balances recombinational repair in Ustilago maydis. Mol Cell Biol 2006; 26:678-88. [PMID: 16382157 PMCID: PMC1346908 DOI: 10.1128/mcb.26.2.678-688.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Rec2 is the single Rad51 paralog in Ustilago maydis. Here, we find that Rec2 is required for radiation-induced Rad51 nuclear focus formation but that Rec2 foci form independently of Rad51 and Brh2. Brh2 foci also form in the absence of Rad51 and Rec2. By coprecipitation from cleared extracts prepared from Escherichia coli cells expressing the proteins, we found that Rec2 interacts physically not only with Rad51 and itself but also with Brh2. Transgenic expression of Brh2 in rec2 mutants can effectively restore radiation resistance, but the frequencies of spontaneous Rad51 focus formation and allelic recombination are elevated. The Dss1-independent Brh2-RPA70 fusion protein is also active in restoring radiation sensitivity of rec2 but is hyperactive to an extreme degree in allelic recombination and in suppressing the meiotic block of rec2. However, the high frequency of chromosome missegregation in meiotic products is an indicator of a corrupted process. The results demonstrate that the importance of Rec2 function is not only in stimulating recombination activity but also in ensuring that recombination is properly controlled.
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Affiliation(s)
- Milorad Kojic
- Department of Microbiology and Immunology, Hearst Microbiology Research Center, Box 62, Cornell University Weill Medical College, 1300 York Avenue, New York, New York 10021, USA
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28
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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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29
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Gruver AM, Miller KA, Rajesh C, Smiraldo PG, Kaliyaperumal S, Balder R, Stiles KM, Albala JS, Pittman DL. The ATPase motif in RAD51D is required for resistance to DNA interstrand crosslinking agents and interaction with RAD51C. Mutagenesis 2005; 20:433-40. [PMID: 16236763 DOI: 10.1093/mutage/gei059] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Homologous recombination (HR) is a mechanism for repairing DNA interstrand crosslinks and double-strand breaks. In mammals, HR requires the activities of the RAD51 family (RAD51, RAD51B, RAD51C, RAD51D, XRCC2, XRCC3 and DMC1), each of which contains conserved ATP binding sequences (Walker Motifs A and B). RAD51D is a DNA-stimulated ATPase that interacts directly with RAD51C and XRCC2. To test the hypothesis that ATP binding and hydrolysis by RAD51D are required for the repair of interstrand crosslinks, site-directed mutations in Walker Motif A were generated, and complementation studies were performed in Rad51d-deficient mouse embryonic fibroblasts. The K113R and K113A mutants demonstrated a respective 96 and 83% decrease in repair capacity relative to wild-type. Further examination of these mutants, by yeast two-hybrid analyses, revealed an 8-fold reduction in the ability to associate with RAD51C whereas interaction with XRCC2 was retained at a level similar to the S111T control. These cell-based studies are the first evidence that ATP binding and hydrolysis by RAD51D are required for efficient HR repair of DNA interstrand crosslinks.
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Affiliation(s)
- Aaron M Gruver
- Department of Physiology and Cardiovascular Genomics, Medical University of Ohio, Toledo, OH 43614-5804, USA
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30
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Zhang XP, Lee KI, Solinger JA, Kiianitsa K, Heyer WD. Gly-103 in the N-terminal domain of Saccharomyces cerevisiae Rad51 protein is critical for DNA binding. J Biol Chem 2005; 280:26303-11. [PMID: 15908697 DOI: 10.1074/jbc.m503244200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rad51 is a homolog of the bacterial RecA protein and is central for recombination in eukaryotes performing homology search and DNA strand exchange. Rad51 and RecA share a core ATPase domain that is structurally similar to the ATPase domains of helicases and the F1 ATPase. Rad51 has an additional N-terminal domain, whereas RecA protein has an additional C-terminal domain. Here we show that glycine 103 in the N-terminal domain of Saccharomyces cerevisiae Rad51 is important for binding to single-stranded and duplex DNA. The Rad51-G103E mutant protein is deficient in DNA strand exchange and ATPase activity due to a primary DNA binding defect. The N-terminal domain of Rad51 is connected to the ATPase core through an extended elbow linker that ensures flexibility of the N-terminal domain. Molecular modeling of the Rad51-G103E mutant protein shows that the negatively charged glutamate residue lies on the surface of the N-terminal domain facing a positively charged patch composed of Arg-260, His-302, and Lys-305 on the ATPase core domain. A possible structural explanation for the DNA binding defect is that a charge interaction between Glu-103 and the positive patch restricts the flexibility of the N-terminal domain. Rad51-G103E was identified in a screen for Rad51 interaction-deficient mutants and was shown to ablate the Rad54 interaction in two-hybrid assays (Krejci, L., Damborsky, J., Thomsen, B., Duno, M., and Bendixen, C. (2001) Mol. Cell. Biol. 21, 966-976). Surprisingly, we found that the physical interaction of Rad51-G103E with Rad54 was not affected. Our data suggest that the two-hybrid interaction defect was an indirect consequence of the DNA binding defect.
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Affiliation(s)
- Xiao-Ping Zhang
- Section of Microbiology, University of California, Davis, California 95616-8665, USA
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