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Sabei A, Prentiss M, Prévost C. Modeling the Homologous Recombination Process: Methods, Successes and Challenges. Int J Mol Sci 2023; 24:14896. [PMID: 37834348 PMCID: PMC10573387 DOI: 10.3390/ijms241914896] [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: 09/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information.
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Affiliation(s)
- Afra Sabei
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA02138, USA;
| | - Chantal Prévost
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
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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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Bueno-Martínez E, Sanoguera-Miralles L, Valenzuela-Palomo A, Lorca V, Gómez-Sanz A, Carvalho S, Allen J, Infante M, Pérez-Segura P, Lázaro C, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. RAD51D Aberrant Splicing in Breast Cancer: Identification of Splicing Regulatory Elements and Minigene-Based Evaluation of 53 DNA Variants. Cancers (Basel) 2021; 13:2845. [PMID: 34200360 PMCID: PMC8201001 DOI: 10.3390/cancers13112845] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
RAD51D loss-of-function variants increase lifetime risk of breast and ovarian cancer. Splicing disruption is a frequent pathogenic mechanism associated with variants in susceptibility genes. Herein, we have assessed the splicing and clinical impact of splice-site and exonic splicing enhancer (ESE) variants identified through the study of ~113,000 women of the BRIDGES cohort. A RAD51D minigene with exons 2-9 was constructed in splicing vector pSAD. Eleven BRIDGES splice-site variants (selected by MaxEntScan) were introduced into the minigene by site-directed mutagenesis and tested in MCF-7 cells. The 11 variants disrupted splicing, collectively generating 25 different aberrant transcripts. All variants but one produced negligible levels (<3.4%) of the full-length (FL) transcript. In addition, ESE elements of the alternative exon 3 were mapped by testing four overlapping exonic microdeletions (≥30-bp), revealing an ESE-rich interval (c.202_235del) with critical sequences for exon 3 recognition that might have been affected by germline variants. Next, 26 BRIDGES variants and 16 artificial exon 3 single-nucleotide substitutions were also assayed. Thirty variants impaired splicing with variable amounts (0-65.1%) of the FL transcript, although only c.202G>A demonstrated a complete aberrant splicing pattern without the FL transcript. On the other hand, c.214T>C increased efficiency of exon 3 recognition, so only the FL transcript was detected (100%). In conclusion, 41 RAD51D spliceogenic variants (28 of which were from the BRIDGES cohort) were identified by minigene assays. We show that minigene-based mapping of ESEs is a powerful approach for identifying ESE hotspots and ESE-disrupting variants. Finally, we have classified nine variants as likely pathogenic according to ACMG/AMP-based guidelines, highlighting the complex relationship between splicing alterations and variant interpretation.
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Affiliation(s)
- Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Alicia Gómez-Sanz
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Mar Infante
- Cancer Genetics, Unidad de Excelencia Instituto de Biología y Genética Molecular (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, 08908 Hospitalet de Llobregat, Spain;
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
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Hogrel G, Lu Y, Alexandre N, Bossé A, Dulermo R, Ishino S, Ishino Y, Flament D. Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea. Biomolecules 2020; 10:E1045. [PMID: 32674430 PMCID: PMC7407445 DOI: 10.3390/biom10071045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Among the three domains of life, the process of homologous recombination (HR) plays a central role in the repair of double-strand DNA breaks and the restart of stalled replication forks. Curiously, main protein actors involved in the HR process appear to be essential for hyperthermophilic Archaea raising interesting questions about the role of HR in replication and repair strategies of those Archaea living in extreme conditions. One key actor of this process is the recombinase RadA, which allows the homologous strand search and provides a DNA substrate required for following DNA synthesis and restoring genetic information. DNA polymerase operation after the strand exchange step is unclear in Archaea. Working with Pyrococcus abyssi proteins, here we show that both DNA polymerases, family-B polymerase (PolB) and family-D polymerase (PolD), can take charge of processing the RadA-mediated recombination intermediates. Our results also indicate that PolD is far less efficient, as compared with PolB, to extend the invaded DNA at the displacement-loop (D-loop) substrate. These observations coincide with previous genetic analyses obtained on Thermococcus species showing that PolB is mainly involved in DNA repair without being essential probably because PolD could take over combined with additional partners.
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Affiliation(s)
- Gaëlle Hogrel
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Yang Lu
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Nicolas Alexandre
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Audrey Bossé
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Rémi Dulermo
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka 819-0395, Japan; (S.I.); (Y.I.)
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka 819-0395, Japan; (S.I.); (Y.I.)
| | - Didier Flament
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
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5
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Vydyam P, Dutta D, Sutram N, Bhattacharyya S, Bhattacharyya MK. A small-molecule inhibitor of the DNA recombinase Rad51 from Plasmodium falciparum synergizes with the antimalarial drugs artemisinin and chloroquine. J Biol Chem 2019; 294:8171-8183. [PMID: 30936202 DOI: 10.1074/jbc.ra118.005009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 03/27/2019] [Indexed: 11/06/2022] Open
Abstract
Malaria parasites repair DNA double-strand breaks (DSBs) primarily through homologous recombination (HR). Here, because the unrepaired DSBs lead to the death of the unicellular parasite Plasmodium falciparum, we investigated its recombinase, PfRad51, as a potential drug target. Undertaking an in silico screening approach, we identified a compound, B02, that docks to the predicted tertiary structure of PfRad51 with high affinity. B02 inhibited a drug-sensitive P. falciparum strain (3D7) and multidrug-resistant parasite (Dd2) in culture, with IC50 values of 8 and 3 μm, respectively. We found that B02 is more potent against these P. falciparum strains than against mammalian cell lines. Our findings also revealed that the antimalarial activity of B02 synergizes with those of two first-line malaria drugs, artemisinin (ART) and chloroquine (CQ), lowering the IC50 values of ART and CQ by 15- and 8-fold, respectively. Our results also provide mechanistic insights into the anti-parasitic activity of B02, indicating that it blocks the ATPase and strand-exchange activities of PfRad51 and abrogates the formation of PfRad51 foci on damaged DNA at chromosomal sites, probably by blocking homomeric interactions of PfRad51 proteins. The B02-mediated PfRad51 disruption led to the accumulation of unrepaired parasitic DNA and rendered parasites more sensitive to DNA-damaging agents, including ART. Our findings provide a rationale for targeting the Plasmodium DSB repair pathway in combination with ART. We propose that identification of a specific inhibitor of HR in Plasmodium may enable investigations of HR's role in Plasmodium biology, including generation of antigenic diversity.
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Affiliation(s)
- Pratap Vydyam
- Department of Biochemistry, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
| | - Dibyendu Dutta
- Department of Biochemistry, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
| | - Niranjan Sutram
- Department of Biochemistry, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
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6
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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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Leite WC, Galvão CW, Saab SC, Iulek J, Etto RM, Steffens MBR, Chitteni-Pattu S, Stanage T, Keck JL, Cox MM. Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament. PLoS One 2016; 11:e0159871. [PMID: 27447485 PMCID: PMC4957752 DOI: 10.1371/journal.pone.0159871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/08/2016] [Indexed: 11/18/2022] Open
Abstract
The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.
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Affiliation(s)
- Wellington C. Leite
- Department of Physics, Ponta Grossa State University (UEPG), Av. Carlos Cavalcanti, 4748, CEP. 84.030–900, Ponta Grossa, PR, Brazil
- * E-mail: (MC); (WL)
| | - Carolina W. Galvão
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Sérgio C. Saab
- Department of Physics, Ponta Grossa State University (UEPG), Av. Carlos Cavalcanti, 4748, CEP. 84.030–900, Ponta Grossa, PR, Brazil
| | - Jorge Iulek
- Department of Chemistry, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Rafael M. Etto
- Department of Chemistry, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Maria B. R. Steffens
- Department of Biochemistry and Molecular Biology, Federal University of Parana, CEP 81531–980 Curitiba, Brazil
| | - Sindhu Chitteni-Pattu
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
| | - Tyler Stanage
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
- * E-mail: (MC); (WL)
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8
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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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Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert CH, Prévost C. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. PLoS One 2015; 10:e0116414. [PMID: 25785454 PMCID: PMC4364692 DOI: 10.1371/journal.pone.0116414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Oligomeric macromolecules in the cell self-organize into a wide variety of geometrical motifs such as helices, rings or linear filaments. The recombinase proteins involved in homologous recombination present many such assembly motifs. Here, we examine in particular the polymorphic characteristics of RecA, the most studied member of the recombinase family, using an integrative approach that relates local modes of monomer/monomer association to the global architecture of their screw-type organization. In our approach, local modes of association are sampled via docking or Monte Carlo simulations. This enables shedding new light on fiber morphologies that may be adopted by the RecA protein. Two distinct RecA helical morphologies, the so-called "extended" and "compressed" forms, are known to play a role in homologous recombination. We investigate the variability within each form in terms of helical parameters and steric accessibility. We also address possible helical discontinuities in RecA filaments due to multiple monomer-monomer association modes. By relating local interface organization to global filament morphology, the strategies developed here to study RecA self-assembly are particularly well suited to other DNA-binding proteins and to filamentous protein assemblies in general.
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Affiliation(s)
- Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Johann Ezelin
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pierre Poulain
- DSIMB team, Inserm UMR-S 665 and Univ. Paris Diderot, Sorbonne Paris Cité, INTS, 6 rue Alexandre Cabanel, 75015 Paris, France
- Ets Poulain, Pointe-Noire, Republic of Congo
| | - Adrien Saladin
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Martin Zacharias
- Technische Universität München, Physik-Department, James-Franck-Str. 1, 85748 Garching, Germany
| | - Charles H. Robert
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- * E-mail:
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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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Mahaney BL, Hammel M, Meek K, Tainer JA, Lees-Miller SP. XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol 2013; 91:31-41. [PMID: 23442139 DOI: 10.1139/bcb-2012-0058] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA double strand breaks (DSBs), induced by ionizing radiation (IR) and endogenous stress including replication failure, are the most cytotoxic form of DNA damage. In human cells, most IR-induced DSBs are repaired by the nonhomologous end joining (NHEJ) pathway. One of the most critical steps in NHEJ is ligation of DNA ends by DNA ligase IV (LIG4), which interacts with, and is stabilized by, the scaffolding protein X-ray cross-complementing gene 4 (XRCC4). XRCC4 also interacts with XRCC4-like factor (XLF, also called Cernunnos); yet, XLF has been one of the least mechanistically understood proteins and precisely how XLF functions in NHEJ has been enigmatic. Here, we examine current combined structural and mutational findings that uncover integrated functions of XRCC4 and XLF and reveal their interactions to form long, helical protein filaments suitable to protect and align DSB ends. XLF-XRCC4 provides a global structural scaffold for ligating DSBs without requiring long DNA ends, thus ensuring accurate and efficient ligation and repair. The assembly of these XRCC4-XLF filaments, providing both DNA end protection and alignment, may commit cells to NHEJ with general biological implications for NHEJ and DSB repair processes and their links to cancer predispositions and interventions.
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Affiliation(s)
- Brandi L Mahaney
- Department of Biochemistry, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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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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13
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Chen LT, Wang AHJ. A rationally designed peptide enhances homologous recombination in vitro and resistance to DNA damaging agents in vivo. Nucleic Acids Res 2010; 38:4361-71. [PMID: 20308162 PMCID: PMC2910059 DOI: 10.1093/nar/gkq182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The RecA family of proteins is essential in homologous recombination, a critical step in DNA repair. Here, we report that a rationally-designed small peptide based on the crystal structure of Escherichia coli RecA–DNA complex can promote homologous recombination through the enhancement of both RecA-mediated strand assimilation and three-strand exchange activity. Among 17 peptides tested, peptide #3 with the amino acid sequence of IRFLTARRR has the most potent activity in promoting the RecA-mediated D-loop formation by ∼7.2-fold at 37°C. Other peptides such as IRFLTAKKK and IRLLTARRR also have similar, albeit lower, activities. Therefore, hydrophobicity and poly-positive charges, and the space between them in those small peptides are crucial features for such activities. The enhancement of recombination by these peptides appears to be a general phenomenon as similar results were seen by using different plasmids. Remarkably, peptide #3 alone without RecA can also promote the D-loop formation at elevated temperature. Cell viability assays showed that the peptide elevates mammalian cell resistance to two cytotoxic DNA drugs, cisplatin and doxorubicin. The rescue of viability may result from increased DNA repair efficiency. Such peptides may find future biological applications.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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14
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Egelman EH, Amos LA. Electron microscopy of helical filaments: rediscovering buried treasures in negative stain. Bioessays 2009; 31:909-11. [PMID: 19642111 DOI: 10.1002/bies.200900075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Although negative stain electron microscopy is a wonderfully simple way of directly visualizing protein complexes and other biological macromolecules, the images are not really comparable to those of objects seen in everyday life. The failure to appreciate this has recently led to an incorrect interpretation of RecA-family filament structures.
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908-0733, USA.
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