1
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Takahashi M, Ito K, Iwasaki H, Norden B. Linear dichroism reveals the perpendicular orientation of DNA bases in the RecA and Rad51 recombinase filaments: A possible mechanism for the strand exchange reaction. Chirality 2024; 36:e23664. [PMID: 38561319 DOI: 10.1002/chir.23664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
Linear dichroism spectroscopy is used to investigate the structure of RecA family recombinase filaments (RecA and Rad51 proteins) with DNA for clarifying the molecular mechanism of DNA strand exchange promoted by these proteins and its activation. The measurements show that the recombinases promote the perpendicular base orientation of single-stranded DNA only in the presence of activators, indicating the importance of base orientation in the reaction. We summarize the results and discuss the role of DNA base orientation.
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Affiliation(s)
- Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kentaro Ito
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hiroshi Iwasaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Innovative Science Institute, Tokyo Institute of Technology, Yokohama, Japan
| | - Bengt Norden
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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2
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Renodon-Corniere A, Mikawa T, Kuwabara N, Ito K, Levitsky D, Iwasaki H, Takahashi M. Human Rad51 Protein Requires Higher Concentrations of Calcium Ions for D-Loop Formation than for Oligonucleotide Strand Exchange. Int J Mol Sci 2024; 25:3633. [PMID: 38612444 PMCID: PMC11011376 DOI: 10.3390/ijms25073633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Human Rad51 protein (HsRad51)-promoted DNA strand exchange, a crucial step in homologous recombination, is regulated by proteins and calcium ions. Both the activator protein Swi5/Sfr1 and Ca2+ ions stimulate different reaction steps and induce perpendicular DNA base alignment in the presynaptic complex. To investigate the role of base orientation in the strand exchange reaction, we examined the Ca2+ concentration dependence of strand exchange activities and structural changes in the presynaptic complex. Our results show that optimal D-loop formation (strand exchange with closed circular DNA) required Ca2+ concentrations greater than 5 mM, whereas 1 mM Ca2+ was sufficient for strand exchange between two oligonucleotides. Structural changes indicated by increased fluorescence intensity of poly(dεA) (a poly(dA) analog) reached a plateau at 1 mM Ca2+. Ca2+ > 2 mM was required for saturation of linear dichroism signal intensity at 260 nm, associated with rigid perpendicular DNA base orientation, suggesting a correlation with the stimulation of D-loop formation. Therefore, Ca2+ exerts two different effects. Thermal stability measurements suggest that HsRad51 binds two Ca2+ ions with KD values of 0.2 and 2.5 mM, implying that one step is stimulated by one Ca2+ bond and the other by two Ca2+ bonds. Our results indicate parallels between the Mg2+ activation of RecA and the Ca2+ activation of HsRad51.
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Affiliation(s)
| | - Tsutomu Mikawa
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan;
| | - Naoyuki Kuwabara
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan;
| | - Kentaro Ito
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan;
| | - Dmitri Levitsky
- Nantes Université, CNRS, US2B, UMR 6286, F-44000 Nantes, France; (A.R.-C.); (D.L.)
| | - Hiroshi Iwasaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan;
- Innovative Science Institute, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan;
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3
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Takahashi M, Norden B. Linear Dichroism Measurements for the Study of Protein-DNA Interactions. Int J Mol Sci 2023; 24:16092. [PMID: 38003280 PMCID: PMC10671323 DOI: 10.3390/ijms242216092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Linear dichroism (LD) is a differential polarized light absorption spectroscopy used for studying filamentous molecules such as DNA and protein filaments. In this study, we review the applications of LD for the analysis of DNA-protein interactions. LD signals can be measured in a solution by aligning the sample using flow-induced shear force or a strong electric field. The signal generated is related to the local orientation of chromophores, such as DNA bases, relative to the filament axis. LD can thus assess the tilt and roll of DNA bases and distinguish intercalating from groove-binding ligands. The intensity of the LD signal depends upon the degree of macroscopic orientation. Therefore, DNA shortening and bending can be detected by a decrease in LD signal intensity. As examples of LD applications, we present a kinetic study of DNA digestion by restriction enzymes and structural analyses of homologous recombination intermediates, i.e., RecA and Rad51 recombinase complexes with single-stranded DNA. LD shows that the DNA bases in these complexes are preferentially oriented perpendicular to the filament axis only in the presence of activators, suggesting the importance of organized base orientation for the reaction. LD measurements detect DNA bending by the CRP transcription activator protein, as well as by the UvrB DNA repair protein. LD can thus provide information about the structures of protein-DNA complexes under various conditions and in real time.
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Affiliation(s)
- Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Oookayama, Meguro, Tokyo 152-8550, Japan
| | - Bengt Norden
- Department of Chemical and Biological Engineering, Chemistry, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
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4
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Hong L, Braden DC, Zhao Y, Skoko JJ, Chang F, Woodcock SR, Uvalle C, Casey A, Wood K, Salvatore SR, Asan A, Harkness T, Fagunloye A, Razzaghi M, Straub A, Spies M, Brown DD, Lee AV, Schopfer F, Freeman BA, Neumann CA. Small molecule nitroalkenes inhibit RAD51-mediated homologous recombination and amplify triple-negative breast cancer cell killing by DNA-directed therapies. Redox Biol 2023; 66:102856. [PMID: 37633047 PMCID: PMC10472314 DOI: 10.1016/j.redox.2023.102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023] Open
Abstract
Nitro fatty acids (NO2-FAs) are endogenously generated lipid signaling mediators from metabolic and inflammatory reactions between conjugated diene fatty acids and nitric oxide or nitrite-derived reactive species. NO2-FAs undergo reversible Michael addition with hyperreactive protein cysteine thiolates to induce posttranslational protein modifications that can impact protein function. Herein, we report a novel mechanism of action of natural and non-natural nitroalkenes structurally similar to (E) 10-nitro-octadec-9-enoic acid (CP-6), recently de-risked by preclinical Investigational New Drug-enabling studies and Phase 1 and Phase 2 clinical trials and found to induce DNA damage in a TNBC xenograft by inhibiting homologous-recombination (HR)-mediated repair of DNA double-strand breaks (DSB). CP-6 specifically targets Cys319, essential in RAD51-controlled HR-mediated DNA DSB repair in cells. A nitroalkene library screen identified two structurally different nitroalkenes, a non-natural fatty acid [(E) 8-nitro-nonadec-7-enoic acid (CP-8)] and a dicarboxylate ester [dimethyl (E)nitro-oct-4-enedioate (CP-23)] superior to CP-6 in TNBC cells killing, synergism with three different inhibitors of the poly ADP-ribose polymerase (PARP) and γ-IR. CP-8 and CP-23 effectively inhibited γ-IR-induced RAD51 foci formation and HR in a GFP-reported assay but did not affect benign human epithelial cells or cell cycle phases. In vivo, CP-8 and CP-23's efficacies diverged as only CP-8 showed promising anticancer activities alone and combined with the PARP inhibitor talazoparib in an HR-proficient TNBC mouse model. As preliminary preclinical toxicology analysis also suggests CP-8 as safe, our data endorse CP-8 as a novel anticancer molecule for treating cancers sensitive to homologous recombination-mediated DNA repair inhibitors.
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Affiliation(s)
- Lisa Hong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Dennis C Braden
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Yaoning Zhao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA; School of Medicine, Tsinghua University, Beijing, China
| | - John J Skoko
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Fei Chang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven R Woodcock
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Crystall Uvalle
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Allison Casey
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Katherine Wood
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alparslan Asan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Trey Harkness
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Adeola Fagunloye
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Mortezaali Razzaghi
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Adam Straub
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Daniel D Brown
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Francisco Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carola A Neumann
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA.
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5
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Luo SC, Yeh MC, Lien YH, Yeh HY, Siao HL, Tu IP, Chi P, Ho MC. A RAD51-ADP double filament structure unveils the mechanism of filament dynamics in homologous recombination. Nat Commun 2023; 14:4993. [PMID: 37591853 PMCID: PMC10435448 DOI: 10.1038/s41467-023-40672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
ATP-dependent RAD51 recombinases play an essential role in eukaryotic homologous recombination by catalyzing a four-step process: 1) formation of a RAD51 single-filament assembly on ssDNA in the presence of ATP, 2) complementary DNA strand-exchange, 3) ATP hydrolysis transforming the RAD51 filament into an ADP-bound disassembly-competent state, and 4) RAD51 disassembly to provide access for DNA repairing enzymes. Of these steps, filament dynamics between the ATP- and ADP-bound states, and the RAD51 disassembly mechanism, are poorly understood due to the lack of near-atomic-resolution information of the ADP-bound RAD51-DNA filament structure. We report the cryo-EM structure of ADP-bound RAD51-DNA filaments at 3.1 Å resolution, revealing a unique RAD51 double-filament that wraps around ssDNA. Structural analysis, supported by ATP-chase and time-resolved cryo-EM experiments, reveals a collapsing mechanism involving two four-protomer movements along ssDNA for mechanical transition between RAD51 single- and double-filament without RAD51 dissociation. This mechanism enables elastic change of RAD51 filament length during structural transitions between ATP- and ADP-states.
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Affiliation(s)
- Shih-Chi Luo
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
| | - Min-Chi Yeh
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Yu-Hsiang Lien
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Huei-Lun Siao
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Peter Chi
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan.
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6
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Hong L, Braden DC, Zhao Y, Skoko JJ, Chang F, Woodcock SR, Uvalle C, Casey A, Wood K, Salvatore SR, Asan A, Harkness T, Fagunloye A, Razzaghi M, Straub A, Spies M, Brown DD, Lee AV, Schopfer F, Freeman BA, Neumann CA. Small molecule nitroalkenes inhibit RAD51-mediated homologous recombination and amplify triple-negative breast cancer cell killing by DNA-directed therapies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552990. [PMID: 37645906 PMCID: PMC10462009 DOI: 10.1101/2023.08.11.552990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Nitro fatty acids (NO 2 -FAs) are endogenously generated lipid signaling mediators from metabolic and inflammatory reactions between conjugated diene fatty acids and nitric oxide or nitrite-derived reactive species. NO 2 -FAs undergo reversible Michael addition with hyperreactive protein cysteine thiolates to induce posttranslational protein modifications that can impact protein function. Herein, we report a novel mechanism of action of natural and non-natural nitroalkenes structurally similar to ( E ) 10-nitro-octadec-9-enoic acid (CP-6), recently de-risked by preclinical Investigational New Drug-enabling studies and Phase 1 and Phase 2 clinical trials and found to induce DNA damage in a TNBC xenograft by inhibiting homologous-recombination (HR)-mediated repair of DNA double-strand breaks (DSB). CP-6 specifically targets Cys319, essential in RAD51-controlled HR-mediated DNA DSB repair in cells. A nitroalkene library screen identified two structurally different nitroalkenes, a non-natural fatty acid [( E ) 8-nitro- nonadec-7-enoic acid (CP-8)] and a dicarboxylate ester [dimethyl ( E )nitro-oct-4-enedioate (CP- 23)] superior to CP-6 in TNBC cells killing, synergism with three different inhibitors of the poly ADP-ribose polymerase (PARP) and γ-IR. CP-8 and CP-23 effectively inhibited γ-IR-induced RAD51 foci formation and HR in a GFP-reported assay but did not affect benign human epithelial cells or cell cycle phases. In vivo, CP-8 and CP-23's efficacies diverged as only CP-8 showed promising anticancer activities alone and combined with the PARP inhibitor talazoparib in an HR-proficient TNBC mouse model. As preliminary preclinical toxicology analysis also suggests CP-8 as safe, our data endorse CP-8 as a novel anticancer molecule for treating cancers sensitive to homologous recombination-mediated DNA repair inhibitors.
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7
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Appleby R, Bollschweiler D, Chirgadze DY, Joudeh L, Pellegrini L. A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly. iScience 2023; 26:106689. [PMID: 37216117 PMCID: PMC10192527 DOI: 10.1016/j.isci.2023.106689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/21/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
The RAD51 ATPase polymerizes on single-stranded DNA to form nucleoprotein filaments (NPFs) that are critical intermediates in the reaction of homologous recombination. ATP binding maintains the NPF in a competent conformation for strand pairing and exchange. Once strand exchange is completed, ATP hydrolysis licenses the filament for disassembly. Here we show that the ATP-binding site of the RAD51 NPF contains a second metal ion. In the presence of ATP, the metal ion promotes the local folding of RAD51 into the conformation required for DNA binding. The metal ion is absent in the ADP-bound RAD51 filament, that rearranges in a conformation incompatible with DNA binding. The presence of the second metal ion explains how RAD51 couples the nucleotide state of the filament to DNA binding. We propose that loss of the second metal ion upon ATP hydrolysis drives RAD51 dissociation from the DNA and weakens filament stability, contributing to NPF disassembly.
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Affiliation(s)
- Robert Appleby
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | | | - Luay Joudeh
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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8
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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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9
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Wei J, Wang X, Dong Y, Zhong X, Ren X, Song R, Ma J, Yu A, Fan Q, Yao J, Shan D, Lv F, Zheng Y, Deng Q, Li X, He Y, Fan S, Zhao C, Wang X, Yuan R, She G. Curcumae Rhizoma - combined with Sparganii Rhizoma in the treatment of liver cancer: Chemical analysis using UPLC-LTQ-Orbitrap MS n, network analysis, and experimental assessment. Front Pharmacol 2022; 13:1027687. [PMID: 36561345 PMCID: PMC9764015 DOI: 10.3389/fphar.2022.1027687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/09/2022] [Indexed: 12/09/2022] Open
Abstract
Objective: Curcumae Rhizoma-Sparganii Rhizoma (CR-SR) is a traditional botanical drug pair that can promote blood circulation, remove blood stasis, and treat tumors in clinics. The aim of the present study was to investigate the therapeutic material basis and potential mechanisms of CR-SR, CR, and SR for the treatment of liver cancer. Method: The chemical profile analyses of CR-SR, CR, and SR were performed by molecular networking and UPLC-LTQ-Orbitrap MSn. The anti-liver cancer activities of CR-SR, CR, and SR were assessed by using a zebrafish xenograft model in vivo for the first time and detected by the HepG2 cell model in vitro. Combining the network analysis and molecular docking, real-time quantitative polymerase chain reaction (RT-qPCR) experiments were undertaken to further explore the mechanisms of CR-SR, CR, and SR for the treatment of liver cancer. Results: In total, 65 components were identified in CR-SR, CR, and SR. Based on the clusters of molecular networking, a total of 12 novel diarylheptanoids were identified from CR-SR and CR. By combining our results with information from the literature, 32 sesquiterpenoids and 21 cyclic dipeptides were identified from CR-SR, CR, and SR. The anti-liver cancer activities were observed in both the drug pair and the single botanical drugs in vitro and in vivo, and the order of activity was CR-SR > CR > SR. They could downregulate the expression of proto-oncogene tyrosine-protein kinase Src (SRC), epidermal growth factor receptor (EGFR), estrogen receptor-α (ESR1), prostaglandin endoperoxide synthase 2 (PTGS2), and amyloid precursor protein (APP). Conclusion: Taken together, the present study provided an experimental basis for the therapeutic material basis and potential molecular mechanisms of CR-SR, CR, and SR. This study provided a novel insight for objective clinical treatment of liver cancer.
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Affiliation(s)
- Jing Wei
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Xiaoping Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Ying Dong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Xiangjian Zhong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Xueyang Ren
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Ruolan Song
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Jiamu Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Axiang Yu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Qiqi Fan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Jianling Yao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Dongjie Shan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Fang Lv
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Yuan Zheng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Qingyue Deng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Xianxian Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Yingyu He
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Shusheng Fan
- State Key Laboratory of Natural Medicines, New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, China Pharmaceutical University, Nanjing, China
| | - Chongjun Zhao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China
| | - Xiuhuan Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China,Beijing Huilongguan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, China,*Correspondence: Xiuhuan Wang, ; Ruijuan Yuan, ; Gaimei She,
| | - Ruijuan Yuan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,*Correspondence: Xiuhuan Wang, ; Ruijuan Yuan, ; Gaimei She,
| | - Gaimei She
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China,Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing, China,*Correspondence: Xiuhuan Wang, ; Ruijuan Yuan, ; Gaimei She,
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10
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Atwell SX, Migliozzi D, Dupont A, Viovy JL, Cappello G. Structural transitions and mechanochemical coupling in the nucleoprotein filament explain homology selectivity and Rad51 protein cooperativity in cellular DNA repair. Phys Rev E 2020; 101:032407. [PMID: 32289957 DOI: 10.1103/physreve.101.032407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/17/2020] [Indexed: 11/07/2022]
Abstract
The nucleoprotein filament (NPF) is the fundamental element of homologous recombination (HR), a major mechanism for the repair of double-strand DNA breaks in the cell. The NPF is made of the damaged DNA strand surrounded by recombinase proteins, and its sensitivity to base-pairing mismatches is a crucial feature that guarantees the fidelity of the repair. The concurrent recombinases are also essential for several steps of HR. In this work, we used torque-sensitive magnetic tweezers to probe and apply mechanical constraints to single nucleoprotein filaments (NPFs). We demonstrated that the NPF undergoes structural transitions from a stretched to a compact state, and we measured the corresponding mechanochemical signatures. Using an active two-state model, we proposed a free-energy landscape for the NPF transition. Using this quantitative model, we explained both how the sensitivity of the NPF to the homology length is regulated by its structural transition and how the cooperativity of Rad51 favors selectivity to relatively long homologous sequences.
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Affiliation(s)
- Scott X Atwell
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Sorbonne Universités, UPMC Univ Paris 06, Unité Mixte de Recherche 168, 75005 Paris, France
| | - Daniel Migliozzi
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Sorbonne Universités, UPMC Univ Paris 06, Unité Mixte de Recherche 168, 75005 Paris, France.,Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Aurélie Dupont
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Sorbonne Universités, UPMC Univ Paris 06, Unité Mixte de Recherche 168, 75005 Paris, France.,Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique, CNRS, F-38000 Grenoble, France
| | - Jean-Louis Viovy
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Sorbonne Universités, UPMC Univ Paris 06, Unité Mixte de Recherche 168, Institut Pierre Gilles de Gennes, MMBM Group, 75005 Paris, France
| | - Giovanni Cappello
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Sorbonne Universités, UPMC Univ Paris 06, Unité Mixte de Recherche 168, 75005 Paris, France.,Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique, CNRS, F-38000 Grenoble, France
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11
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Wright WD, Shah SS, Heyer WD. Homologous recombination and the repair of DNA double-strand breaks. J Biol Chem 2018; 293:10524-10535. [PMID: 29599286 DOI: 10.1074/jbc.tm118.000372] [Citation(s) in RCA: 410] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination enables the cell to access and copy intact DNA sequence information in trans, particularly to repair DNA damage affecting both strands of the double helix. Here, we discuss the DNA transactions and enzymatic activities required for this elegantly orchestrated process in the context of the repair of DNA double-strand breaks in somatic cells. This includes homology search, DNA strand invasion, repair DNA synthesis, and restoration of intact chromosomes. Aspects of DNA topology affecting individual steps are highlighted. Overall, recombination is a dynamic pathway with multiple metastable and reversible intermediates designed to achieve DNA repair with high fidelity.
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Affiliation(s)
| | | | - Wolf-Dietrich Heyer
- From the Departments of Microbiology and Molecular Genetics and .,Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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12
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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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13
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Vašák M, Schnabl J. Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Met Ions Life Sci 2016; 16:259-90. [DOI: 10.1007/978-3-319-21756-7_8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Ghosh S, Dixit H, Chakrabarti R. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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15
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Sun L, Frykholm K, Fornander LH, Svedhem S, Westerlund F, Akerman B. Sensing conformational changes in DNA upon ligand binding using QCM-D. Polyamine condensation and Rad51 extension of DNA layers. J Phys Chem B 2014; 118:11895-904. [PMID: 25197950 DOI: 10.1021/jp506733w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59-184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59 bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film deformation allows comparative studies of two or more analytes using the same DNA layer as demonstrated here by spermine and spermidine.
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Affiliation(s)
- Lu Sun
- Department of Chemical and Biological Engineering and ‡Department of Applied Physics, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
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16
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Normand A, Rivière E, Renodon-Cornière A. Identification and characterization of human Rad51 inhibitors by screening of an existing drug library. Biochem Pharmacol 2014; 91:293-300. [PMID: 25124703 DOI: 10.1016/j.bcp.2014.07.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022]
Abstract
Homologous Recombination (HR) plays an essential role in cellular proliferation and in maintaining genomic stability by repairing DNA double-stranded breaks that appear during replication. Rad51, a key protein of HR in eukaryotes, can have an elevated expression level in tumor cells, which correlates with their resistance to anticancer therapies. Therefore, targeted inhibition of Rad51 through inhibitor may improve the tumor response to these therapies. In order to identify small molecules that inhibit Rad51 activity, we screened the Prestwick Library (1120 molecules) for their effect on the strand exchange reaction catalyzed by Rad51. We found that Chicago Sky Blue (CSB) is a potent inhibitor of Rad51, showing IC₅₀ values in the low nanomolar range (400 nM). Biochemical analysis demonstrated that the inhibitory mechanism probably occurs by disrupting the Rad51 association with the single-stranded DNA, which prevents the nucleoprotein filament formation, the first step of the protein activity. Structure Activity Relationship analysis with a number of compounds that shared structure homology with CSB was also performed. The sensitivity of Rad51 inhibition to CSB modifications suggests specific interactions between the molecule and Rad51 nucleofilament. CSB and some of its analogs open up new perspectives in the search for agents capable of potentiating chemo- and radio-therapy treatments for cancer. Moreover, these compounds may be excellent tools to analyze Rad51 cellular functions. Our study also highlights how CSB and its analogs, which are frequently used in colorants, stains and markers, could be responsible of unwanted side effects by perturbing the DNA repair process.
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Affiliation(s)
- Anaïs Normand
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France
| | - Emmanuelle Rivière
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France
| | - Axelle Renodon-Cornière
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France.
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17
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Fornander LH, Feng B, Beke-Somfai T, Nordén B. UV Transition Moments of Tyrosine. J Phys Chem B 2014; 118:9247-57. [DOI: 10.1021/jp5065352] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Louise H. Fornander
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bobo Feng
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Tamás Beke-Somfai
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bengt Nordén
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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18
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Stephenson M, Reichardt C, Pinto M, Wächtler M, Sainuddin T, Shi G, Yin H, Monro S, Sampson E, Dietzek B, McFarland SA. Ru(II) dyads derived from 2-(1-pyrenyl)-1H-imidazo[4,5-f][1,10]phenanthroline: versatile photosensitizers for photodynamic applications. J Phys Chem A 2014; 118:10507-21. [PMID: 24927113 DOI: 10.1021/jp504330s] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combining the best attributes of organic photosensitizers with those of coordination complexes is an elegant way to achieve prolonged excited state lifetimes in Ru(II) dyads. Not only do their reduced radiative and nonradiative rates provide ample time for photosensitization of reactive oxygen species at low oxygen tension but they also harness the unique properties of (3)IL states that can act as discrete units or in concert with (3)MLCT states. The imidazo[4,5-f][1,10]phenanthroline framework provides a convenient tether for linking π-expansive ligands such as pyrene to a Ru(II) scaffold, and the stabilizing coligands can fine-tune the chemical and biological properties of these bichromophoric systems. The resulting dyads described in this study exhibited nanomolar light cytotoxicities against cancer cells with photocytotoxicity indices exceeding 400 for some coligands employed. This potency extended to bacteria, where concentrations as low as 10 nM destroyed 75% of a bacterial population. Notably, these dyads remained extremely active against biofilm with light photocytotoxicities against these more resistant bacterial populations in the 10-100 nM regime. The results from this study demonstrate the versatility of these highly potent photosensitizers in destroying both cancer and bacterial cells and expand the scope of compounds that utilize low-lying (3)IL states for photobiological applications.
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Affiliation(s)
- Mat Stephenson
- Department of Chemistry, Acadia University , Wolfville, NS B4P 2R6, Canada
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19
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Fornander LH, Renodon-Cornière A, Kuwabara N, Ito K, Tsutsui Y, Shimizu T, Iwasaki H, Nordén B, Takahashi M. Swi5-Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament. Nucleic Acids Res 2013; 42:2358-65. [PMID: 24304898 PMCID: PMC3936755 DOI: 10.1093/nar/gkt1257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Swi5-Sfr1 heterodimer protein stimulates the Rad51-promoted DNA strand exchange reaction, a crucial step in homologous recombination. To clarify how this accessory protein acts on the strand exchange reaction, we have analyzed how the structure of the primary reaction intermediate, the Rad51/single-stranded DNA (ssDNA) complex filament formed in the presence of ATP, is affected by Swi5-Sfr1. Using flow linear dichroism spectroscopy, we observe that the nucleobases of the ssDNA are more perpendicularly aligned to the filament axis in the presence of Swi5-Sfr1, whereas the bases are more randomly oriented in the absence of Swi5-Sfr1. When using a modified version of the natural protein where the N-terminal part of Sfr1 is deleted, which has no affinity for DNA but maintained ability to stimulate the strand exchange reaction, we still observe the improved perpendicular DNA base orientation. This indicates that Swi5-Sfr1 exerts its activating effect through interaction with the Rad51 filament mainly and not with the DNA. We propose that the role of a coplanar alignment of nucleobases induced by Swi5-Sfr1 in the presynaptic Rad51/ssDNA complex is to facilitate the critical matching with an invading double-stranded DNA, hence stimulating the strand exchange reaction.
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Affiliation(s)
- Louise H Fornander
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden, Research Unit FRE3478, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France, Graduate School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan, Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, KEK, Tsukuba, 305-0801, Japan and Department of Life Science, Graduate School of Bioscience & Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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20
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Cornejo-García JA, Liou LB, Blanca-López N, Doña I, Chen CH, Chou YC, Chuang HP, Wu JY, Chen YT, Plaza-Serón MDC, Mayorga C, Guéant-Rodríguez RM, Lin SC, Torres MJ, Campo P, Rondón C, Laguna JJ, Fernández J, Guéant JL, Canto G, Blanca M, Lee MTM. Genome-wide association study in NSAID-induced acute urticaria/angioedema in Spanish and Han Chinese populations. Pharmacogenomics 2013; 14:1857-69. [PMID: 24236485 DOI: 10.2217/pgs.13.166] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
AIM Acute urticaria/angioedema (AUA) induced by cross-intolerance to NSAIDs is the most frequent clinical entity in hypersensitivity reactions to drugs. In this work, we conducted a genome-wide association study in Spanish and Han Chinese patients suffering from NSAID-induced AUA. MATERIALS & METHODS A whole-genome scan was performed on a total of 232 cases (112 Spanish and 120 Han Chinese) with NSAID-induced AUA and 225 unrelated controls (124 Spanish and 101 Han Chinese). RESULTS Although no polymorphism reached genome-wide significance, we obtained suggestive associations for three clusters in the Spanish group (RIMS1, BICC1 and RAD51L 1) and one region in the Han Chinese population (ABI3BP). Five regions showed suggestive associations after meta-analysis: HLF, RAD51L1, COL24A1, GalNAc-T13 and FBXL7. A majority of these genes are related to Ca(2+), cAMP and/or P53 signaling pathways. CONCLUSION The associations described were different from those related to the metabolism of arachidonic acid and could provide new mechanisms underlying NSAID-induced AUA.
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21
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Molecular modeling and molecular dynamics simulations of recombinase Rad51. Biophys J 2013; 104:1556-65. [PMID: 23561532 DOI: 10.1016/j.bpj.2013.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/29/2013] [Accepted: 02/07/2013] [Indexed: 11/24/2022] Open
Abstract
The Rad51 ATPase plays central roles in DNA homologous recombination. Yeast Rad51 dimer structure in the active form of the filament was constructed using homology modeling techniques, and all-atom molecular dynamics (MD) simulations were performed using the modeled structure. We found two crucial interaction networks involving ATP: one is among the γ-phosphate of ATP, K(+) ions, H352, and D374; the other is among the adenine ring of ATP, R228, and P379. Multiple MD simulations were performed in which the number of bound K(+) ions was changed. The simulated structures suggested that K(+) ions are indispensable for the stabilization of the active dimer and resemble the arginine and lysine fingers of other P-loop containing ATPases and GTPases. MD simulations also showed that the adenine ring of ATP mediates interactions between adjacent protomers. Furthermore, in MD simulations starting from a structure just after ATP hydrolysis, the opening motion corresponding to dissociation from DNA was observed. These results support the hypothesis that ATP and K(+) ions function as glue between protomers.
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22
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Lee M, Lipfert J, Sanchez H, Wyman C, Dekker NH. Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament. Nucleic Acids Res 2013; 41:7023-30. [PMID: 23703213 PMCID: PMC3737536 DOI: 10.1093/nar/gkt425] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Human RAD51 is a key protein in the repair of DNA by homologous recombination. Its assembly onto DNA, which induces changes in DNA structure, results in the formation of a nucleoprotein filament that forms the basis of strand exchange. Here, we determine the structural and mechanical properties of RAD51-dsDNA filaments. Our measurements use two recently developed magnetic tweezers assays, freely orbiting magnetic tweezers and magnetic torque tweezers, designed to measure the twist and torque of individual molecules. By directly monitoring changes in DNA twist on RAD51 binding, we determine the unwinding angle per RAD51 monomer to be 45°, in quantitative agreement with that of its bacterial homolog, RecA. Measurements of the torque that is built up when RAD51-dsDNA filaments are twisted show that under conditions that suppress ATP hydrolysis the torsional persistence length of the RAD51-dsDNA filament exceeds that of its RecA counterpart by a factor of three. Examination of the filament’s torsional stiffness for different combinations of divalent ions and nucleotide cofactors reveals that the Ca2+ ion, apart from suppressing ATPase activity, plays a key role in increasing the torsional stiffness of the filament. These quantitative measurements of RAD51-imposed DNA distortions and accumulated mechanical stress suggest a finely tuned interplay between chemical and mechanical interactions within the RAD51 nucleoprotein filament.
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Affiliation(s)
- Mina Lee
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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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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Nimonkar AV, Dombrowski CC, Siino JS, Stasiak AZ, Stasiak A, Kowalczykowski SC. Saccharomyces cerevisiae Dmc1 and Rad51 proteins preferentially function with Tid1 and Rad54 proteins, respectively, to promote DNA strand invasion during genetic recombination. J Biol Chem 2012; 287:28727-37. [PMID: 22761450 DOI: 10.1074/jbc.m112.373290] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The Saccharomyces cerevisiae Dmc1 and Tid1 proteins are required for the pairing of homologous chromosomes during meiotic recombination. This pairing is the precursor to the formation of crossovers between homologs, an event that is necessary for the accurate segregation of chromosomes. Failure to form crossovers can have serious consequences and may lead to chromosomal imbalance. Dmc1, a meiosis-specific paralog of Rad51, mediates the pairing of homologous chromosomes. Tid1, a Rad54 paralog, although not meiosis-specific, interacts with Dmc1 and promotes crossover formation between homologs. In this study, we show that purified Dmc1 and Tid1 interact physically and functionally. Dmc1 forms stable nucleoprotein filaments that can mediate DNA strand invasion. Tid1 stimulates Dmc1-mediated formation of joint molecules. Under conditions optimal for Dmc1 reactions, Rad51 is specifically stimulated by Rad54, establishing that Dmc1-Tid1 and Rad51-Rad54 function as specific pairs. Physical interaction studies show that specificity in function is not dictated by direct interactions between the proteins. Our data are consistent with the hypothesis that Rad51-Rad54 function together to promote intersister DNA strand exchange, whereas Dmc1-Tid1 tilt the bias toward interhomolog DNA strand exchange.
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Affiliation(s)
- Amitabh V Nimonkar
- Department of Microbiology, University of California, Davis, California 95616, USA
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