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Jurkovic CM, Raisch J, Tran S, Nguyen HD, Lévesque D, Scott MS, Campos EI, Boisvert FM. Replisome Proximal Protein Associations and Dynamic Proteomic Changes at Stalled Replication Forks. Mol Cell Proteomics 2024; 23:100767. [PMID: 38615877 PMCID: PMC11101681 DOI: 10.1016/j.mcpro.2024.100767] [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: 08/16/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024] Open
Abstract
DNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events, we can better grasp the complex and dynamic molecular mechanisms that facilitate DNA replication and repair. Proximity-dependent biotin identification was used to identify associations with 17 proteins within four core replication components, namely the CDC45/MCM2-7/GINS helicase that unwinds DNA, the DNA polymerases, replication protein A subunits, and histone chaperones needed to disassemble and reassemble chromatin. We further investigated the impact of genotoxic stress on these interactions. This analysis revealed a vast proximity association network with 108 nuclear proteins further modulated in the presence of hydroxyurea; 45 being enriched and 63 depleted. Interestingly, hydroxyurea treatment also caused a redistribution of associations with 11 interactors, meaning that the replisome is dynamically reorganized when stressed. The analysis identified several poorly characterized proteins, thereby uncovering new putative players in the cellular response to DNA replication arrest. It also provides a new comprehensive proteomic framework to understand how cells respond to obstacles during DNA replication.
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Affiliation(s)
- Carla-Marie Jurkovic
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jennifer Raisch
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Stephanie Tran
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Hoang Dong Nguyen
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Lévesque
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
| | - François-Michel Boisvert
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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Kaushik V, Chadda R, Kuppa S, Pokhrel N, Vayyeti A, Grady S, Arnatt C, Antony E. Fluorescent human RPA to track assembly dynamics on DNA. Methods 2024; 223:95-105. [PMID: 38301751 PMCID: PMC10923064 DOI: 10.1016/j.ymeth.2024.01.019] [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: 11/01/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
DNA metabolic processes including replication, repair, recombination, and telomere maintenance occur on single-stranded DNA (ssDNA). In each of these complex processes, dozens of proteins function together on the ssDNA template. However, when double-stranded DNA is unwound, the transiently open ssDNA is protected and coated by the high affinity heterotrimeric ssDNA binding Replication Protein A (RPA). Almost all downstream DNA processes must first remodel/remove RPA or function alongside to access the ssDNA occluded under RPA. Formation of RPA-ssDNA complexes trigger the DNA damage checkpoint response and is a key step in activating most DNA repair and recombination pathways. Thus, in addition to protecting the exposed ssDNA, RPA functions as a gatekeeper to define functional specificity in DNA maintenance and genomic integrity. RPA achieves functional dexterity through a multi-domain architecture utilizing several DNA binding and protein-interaction domains connected by flexible linkers. This flexible and modular architecture enables RPA to adopt a myriad of configurations tailored for specific DNA metabolic roles. To experimentally capture the dynamics of the domains of RPA upon binding to ssDNA and interacting proteins we here describe the generation of active site-specific fluorescent versions of human RPA (RPA) using 4-azido-L-phenylalanine (4AZP) incorporation and click chemistry. This approach can also be applied to site-specific modifications of other multi-domain proteins. Fluorescence-enhancement through non-canonical amino acids (FEncAA) and Förster Resonance Energy Transfer (FRET) assays for measuring dynamics of RPA on DNA are also described. The fluorescent human RPA described here will enable high-resolution structure-function analysis of RPA-ssDNA interactions.
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Affiliation(s)
- Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Abhinav Vayyeti
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Scott Grady
- Department of Chemistry, St. Louis University, St. Louis, MO 63103, USA
| | - Chris Arnatt
- Department of Chemistry, St. Louis University, St. Louis, MO 63103, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA.
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Muhammad AA, Basto C, Peterlini T, Guirouilh-Barbat J, Thomas M, Veaute X, Busso D, Lopez B, Mazon G, Le Cam E, Masson JY, Dupaigne P. Human RAD52 stimulates the RAD51-mediated homology search. Life Sci Alliance 2024; 7:e202201751. [PMID: 38081641 PMCID: PMC10713436 DOI: 10.26508/lsa.202201751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Homologous recombination (HR) is a DNA repair mechanism of double-strand breaks and blocked replication forks, involving a process of homology search leading to the formation of synaptic intermediates that are regulated to ensure genome integrity. RAD51 recombinase plays a central role in this mechanism, supported by its RAD52 and BRCA2 partners. If the mediator function of BRCA2 to load RAD51 on RPA-ssDNA is well established, the role of RAD52 in HR is still far from understood. We used transmission electron microscopy combined with biochemistry to characterize the sequential participation of RPA, RAD52, and BRCA2 in the assembly of the RAD51 filament and its activity. Although our results confirm that RAD52 lacks a mediator activity, RAD52 can tightly bind to RPA-coated ssDNA, inhibit the mediator activity of BRCA2, and form shorter RAD51-RAD52 mixed filaments that are more efficient in the formation of synaptic complexes and D-loops, resulting in more frequent multi-invasions as well. We confirm the in situ interaction between RAD51 and RAD52 after double-strand break induction in vivo. This study provides new molecular insights into the formation and regulation of presynaptic and synaptic intermediates by BRCA2 and RAD52 during human HR.
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Affiliation(s)
- Ali Akbar Muhammad
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Clara Basto
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Thibaut Peterlini
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Josée Guirouilh-Barbat
- https://ror.org/02vjkv261 INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, Université de Paris, Paris, France
| | - Melissa Thomas
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Xavier Veaute
- https://ror.org/02vjkv261 CIGEx Platform, INSERM, IRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Didier Busso
- https://ror.org/02vjkv261 CIGEx Platform, INSERM, IRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Bernard Lopez
- https://ror.org/02vjkv261 INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, Université de Paris, Paris, France
| | - Gerard Mazon
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Eric Le Cam
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Pauline Dupaigne
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
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Fousek-Schuller VJ, Borgstahl GEO. The Intriguing Mystery of RPA Phosphorylation in DNA Double-Strand Break Repair. Genes (Basel) 2024; 15:167. [PMID: 38397158 PMCID: PMC10888239 DOI: 10.3390/genes15020167] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle.
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Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
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5
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Kaushik V, Chadda R, Kuppa S, Pokhrel N, Vayyeti A, Grady S, Arnatt C, Antony E. Fluorescent human RPA to track assembly dynamics on DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568455. [PMID: 38045304 PMCID: PMC10690285 DOI: 10.1101/2023.11.23.568455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
DNA metabolic processes including replication, repair, recombination, and telomere maintenance occur on single-stranded DNA (ssDNA). In each of these complex processes, dozens of proteins function together on the ssDNA template. However, when double-stranded DNA is unwound, the transiently open ssDNA is protected and coated by the high affinity heterotrimeric ssDNA binding Replication Protein A (RPA). Almost all downstream DNA processes must first remodel/remove RPA or function alongside to access the ssDNA occluded under RPA. Formation of RPA-ssDNA complexes trigger the DNA damage checkpoint response and is a key step in activating most DNA repair and recombination pathways. Thus, in addition to protecting the exposed ssDNA, RPA functions as a gatekeeper to define functional specificity in DNA maintenance and genomic integrity. RPA achieves functional dexterity through a multi-domain architecture utilizing several DNA binding and protein-interaction domains connected by flexible linkers. This flexible and modular architecture enables RPA to adopt a myriad of configurations tailored for specific DNA metabolic roles. To experimentally capture the dynamics of the domains of RPA upon binding to ssDNA and interacting proteins we here describe the generation of active site-specific fluorescent versions of human RPA (RPA) using 4-azido-L-phenylalanine (4AZP) incorporation and click chemistry. This approach can also be applied to site-specific modifications of other multi-domain proteins. Fluorescence-enhancement through non-canonical amino acids (FEncAA) and Förster Resonance Energy Transfer (FRET) assays for measuring dynamics of RPA on DNA are also described.
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Affiliation(s)
- Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Abhinav Vayyeti
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | - Scott Grady
- Department of Chemistry, St. Louis University, St. Louis, MO 63103
| | - Chris Arnatt
- Department of Chemistry, St. Louis University, St. Louis, MO 63103
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
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Trouillard O, Dupaigne P, Dunoyer M, Doulazmi M, Herlin MK, Frismand S, Riou A, Legros V, Chevreux G, Veaute X, Busso D, Fouquet C, Saint-Martin C, Méneret A, Trembleau A, Dusart I, Dubacq C, Roze E. Congenital mirror movements are associated with defective polymerisation of RAD51. J Med Genet 2023; 60:1116-1126. [PMID: 37308287 DOI: 10.1136/jmg-2023-109189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/21/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Mirror movements are involuntary movements of one hand that mirror intentional movements of the other hand. Congenital mirror movements (CMM) is a rare genetic disorder with autosomal dominant inheritance, in which mirror movements are the main neurological manifestation. CMM is associated with an abnormal decussation of the corticospinal tract, a major motor tract for voluntary movements. RAD51 is known to play a key role in homologous recombination with a critical function in DNA repair. While RAD51 haploinsufficiency was first proposed to explain CMM, other mechanisms could be involved. METHODS We performed Sanger sequencing of RAD51 in five newly identified CMM families to identify new pathogenic variants. We further investigated the expression of wild-type and mutant RAD51 in the patients' lymphoblasts at mRNA and protein levels. We then characterised the functions of RAD51 altered by non-truncating variants using biochemical approaches. RESULTS The level of wild-type RAD51 protein was lower in the cells of all patients with CMM compared with their non-carrier relatives. The reduction was less pronounced in asymptomatic carriers. In vitro, mutant RAD51 proteins showed loss-of-function for polymerisation, DNA binding and strand exchange activity. CONCLUSION Our study demonstrates that RAD51 haploinsufficiency, including loss-of-function of non-truncating variants, results in CMM. The incomplete penetrance likely results from post-transcriptional compensation. Changes in RAD51 levels and/or polymerisation properties could influence guidance of the corticospinal axons during development. Our findings open up new perspectives to understand the role of RAD51 in neurodevelopment.
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Affiliation(s)
- Oriane Trouillard
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Margaux Dunoyer
- Hôpital Pitié-Salpêtrière, Département de Neurologie, AP-HP, Paris, France
| | - Mohamed Doulazmi
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Biological Adaptation and Ageing, B2A, Sorbonne Université, F-75005 Paris, France
| | - Morten Krogh Herlin
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Audrey Riou
- Service de génétique clinique & Service de neurologie, CHU Rennes, Rennes, France
| | - Véronique Legros
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Guillaume Chevreux
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Xavier Veaute
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, CIGEx/iRCM/IBFJ, Université Paris Cité, F-92260 Fontenay-aux-Roses, France
| | - Didier Busso
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, CIGEx/iRCM/IBFJ, Université Paris Cité, F-92260 Fontenay-aux-Roses, France
| | - Coralie Fouquet
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Cécile Saint-Martin
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique Médicale, Sorbonne Université, Paris, France
| | - Aurélie Méneret
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
- Hôpital Pitié-Salpêtrière, DMU Neuroscience 6, AP-HP, Paris, France
| | - Alain Trembleau
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Isabelle Dusart
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Caroline Dubacq
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Emmanuel Roze
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
- Hôpital Pitié-Salpêtrière, DMU Neuroscience 6, AP-HP, Paris, France
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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8
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Feltes BC. Every protagonist has a sidekick: Structural aspects of human xeroderma pigmentosum-binding proteins in nucleotide excision repair. Protein Sci 2021; 30:2187-2205. [PMID: 34420242 DOI: 10.1002/pro.4173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022]
Abstract
The seven xeroderma pigmentosum proteins (XPps), XPA-XPG, coordinate the nucleotide excision repair (NER) pathway, promoting the excision of DNA lesions caused by exposition to ionizing radiation, majorly from ultraviolet light. Significant efforts are made to investigate NER since mutations in any of the seven XPps may cause the xeroderma pigmentosum and trichothiodystrophy diseases. However, these proteins collaborate with other pivotal players in all known NER steps to accurately exert their purposes. Therefore, in the old and ever-evolving field of DNA repair, it is imperative to reexamine and describe their structures to understand NER properly. This work provides an up-to-date review of the protein structural aspects of the closest partners that directly interact and influence XPps: RAD23B, CETN2, DDB1, RPA (RPA70, 32, and 14), p8 (GTF2H5), and ERCC1. Structurally and functionally vital domains, regions, and critical residues are reexamined, providing structural lessons and perspectives about these indispensable proteins in the NER and other DNA repair pathways. By gathering all data related to the major human xeroderma pigmentosum-interacting proteins, this review will aid newcomers on the subject and guide structural and functional future studies.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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9
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Ribeiro J, Dupaigne P, Petrillo C, Ducrot C, Duquenne C, Veaute X, Saintomé C, Busso D, Guerois R, Martini E, Livera G. The meiosis-specific MEIOB-SPATA22 complex cooperates with RPA to form a compacted mixed MEIOB/SPATA22/RPA/ssDNA complex. DNA Repair (Amst) 2021; 102:103097. [PMID: 33812231 DOI: 10.1016/j.dnarep.2021.103097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/30/2022]
Abstract
During meiosis, programmed double-strand breaks are repaired by homologous recombination (HR) to form crossovers that are essential to homologous chromosome segregation. Single-stranded DNA (ssDNA) containing intermediates are key features of HR, which must be highly regulated. RPA, the ubiquitous ssDNA binding complex, was thought to play similar roles during mitotic and meiotic HR until the recent discovery of MEIOB and its partner, SPATA22, two essential meiosis-specific proteins. Here, we show that like MEIOB, SPATA22 resembles RPA subunits and binds ssDNA. We studied the physical and functional interactions existing between MEIOB, SPATA22, and RPA, and show that MEIOB and SPATA22 interact with the preformed RPA complex through their interacting domain and condense RPA-coated ssDNA in vitro. In meiotic cells, we show that MEIOB and SPATA22 modify the immunodetection of the two large subunits of RPA. Given these results, we propose that MEIOB-SPATA22 and RPA form a functional ssDNA-interacting complex to satisfy meiotic HR requirements by providing specific properties to the ssDNA.
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Affiliation(s)
- Jonathan Ribeiro
- Laboratory of Development of the Gonads, UMR E008 Genetic Stability Stem Cells and Radiations, Université de Paris, Université Paris Saclay, CEA, F-92265, Fontenay aux Roses, France
| | - Pauline Dupaigne
- Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126, Interactions Moléculaires et Cancer, CNRS, Université Paris Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Cynthia Petrillo
- Laboratory of Development of the Gonads, UMR E008 Genetic Stability Stem Cells and Radiations, Université de Paris, Université Paris Saclay, CEA, F-92265, Fontenay aux Roses, France
| | - Cécile Ducrot
- Laboratory of Development of the Gonads, UMR E008 Genetic Stability Stem Cells and Radiations, Université de Paris, Université Paris Saclay, CEA, F-92265, Fontenay aux Roses, France
| | - Clotilde Duquenne
- Laboratory of Development of the Gonads, UMR E008 Genetic Stability Stem Cells and Radiations, Université de Paris, Université Paris Saclay, CEA, F-92265, Fontenay aux Roses, France
| | - Xavier Veaute
- CIGEx, UMRE008 Stabilité Génétique Cellules Souches et Radiations, Université de Paris, Université Paris-Saclay, CEA, Inserm, U1274, F-92260, Fontenay-aux-Roses, France
| | - Carole Saintomé
- MNHN, CNRS UMR 7196, INSERM U1154, Sorbonne Universités, 75231, Paris, France
| | - Didier Busso
- CIGEx, UMRE008 Stabilité Génétique Cellules Souches et Radiations, Université de Paris, Université Paris-Saclay, CEA, Inserm, U1274, F-92260, Fontenay-aux-Roses, France
| | - Raphaël Guerois
- CNRS I2BC UMR 9198, iBiTec-S, SB²SM CEA SACLAY, 91191, Gif sur Yvette, France
| | - Emmanuelle Martini
- Laboratory of Development of the Gonads, UMR E008 Genetic Stability Stem Cells and Radiations, Université de Paris, Université Paris Saclay, CEA, F-92265, Fontenay aux Roses, France.
| | - Gabriel Livera
- Laboratory of Development of the Gonads, UMR E008 Genetic Stability Stem Cells and Radiations, Université de Paris, Université Paris Saclay, CEA, F-92265, Fontenay aux Roses, France
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10
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Rechkunova NI, Lavrik OI. Photoreactive DNA as a Tool to Study Replication Protein A Functioning in DNA Replication and Repair. Photochem Photobiol 2020; 96:440-449. [PMID: 32017119 DOI: 10.1111/php.13222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/08/2019] [Indexed: 11/30/2022]
Abstract
Replication protein A (RPA), eukaryotic single-stranded DNA-binding protein, is a key player in multiple processes of DNA metabolism including DNA replication, recombination and DNA repair. Human RPA composed of subunits of 70-, 32- and 14-kDa binds ssDNA with high affinity and interacts specifically with multiple proteins. The RPA heterotrimer binds ssDNA in several modes, with occlusion lengths of 8-10, 13-22 and 30 nucleotides corresponding to global, transitional and elongated conformations of protein. Varying the structure of photoreactive DNA, the intermediates of different stages of DNA replication or DNA repair were designed and applied to identify positioning of the RPA subunits on the specific DNA structures. Using this approach, RPA interactions with various types of DNA structures attributed to replication and DNA repair intermediates were examined. This review is dedicated to blessed memory of Prof. Alain Favre who contributed to the development of photoreactive nucleotide derivatives and their application for the study of protein-nucleic acids interactions.
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Affiliation(s)
- Nadejda I Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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11
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Gérard-Hirne T, Thiebaut F, Sachon E, Désert A, Drujon T, Guérineau V, Michel BY, Benhida R, Coulon S, Saintomé C, Guianvarc'h D. Photoactivatable oligonucleotide probes to trap single-stranded DNA binding proteins: Updating the potential of 4-thiothymidine from a comparative study. Biochimie 2018; 154:164-175. [PMID: 30171884 DOI: 10.1016/j.biochi.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023]
Abstract
Photoaffinity labeling (PAL) in combination with recent developments in mass spectrometry is a powerful tool for studying nucleic acid-protein interactions, enabling crosslinking of both partners through covalent bond formation. Such a strategy requires a preliminary study of the most judicious photoreactive group to crosslink efficiently with the target protein. In this study, we report a survey of three different photoreactive nucleobases (including a guanine functionalized with a benzophenone or a diazirine and the zero-length agent 4-thiothymine) incorporated in 30-mer oligonucleotides (ODN) containing a biotin moiety for selective trapping and enrichment of single-stranded DNA binding proteins (SSB). First, the conditions and efficiency of the photochemical reaction with a purified protein using human replication protein A as the relevant model was studied. Secondly, the ability of the probe as bait to photocrosslink and enrich SSB in cell lysate was addressed. Among the different ODN probes studied, we showed that 4-thiothymine was the most relevant: i) it allows efficient and specific trapping of SSB in whole cell extracts in a similar extent as the widely used diazirine, ii) it features the advantages of a zero-length agent thus retaining the physicochemical properties of the ODN bait; iii) ODN including this photochemical agent are easily accessible. In combination with mass spectrometry, the probes incorporating this nucleobase are powerful tools for PAL strategies and can be added in the toolbox of the traditional photocrosslinkers for studying DNA-protein interactions.
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Affiliation(s)
- Tom Gérard-Hirne
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Frédéric Thiebaut
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; MNHN CNRS UMR 7196, INSERM U1154, 43 Rue Cuvier, 75005, Paris, France
| | - Emmanuelle Sachon
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; Plateforme de spectrométrie de masse et protéomique, IBPS, FR3631, UPMC, 4 Place Jussieu, 75005, Paris, France
| | - Alexandre Désert
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Thierry Drujon
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Benoît Y Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France
| | - Stéphane Coulon
- CRCM, CNRS, Inserm, Aix-Marseille Univ, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Carole Saintomé
- MNHN CNRS UMR 7196, INSERM U1154, 43 Rue Cuvier, 75005, Paris, France; Sorbonne Université, UFR927, 4, Place Jussieu, F-75005, Paris, France.
| | - Dominique Guianvarc'h
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; Institut de Chimie Moléculaire et des Matériaux d'Orsay, Univ. Paris-Sud, CNRS, Université Paris-Saclay, F-91405, Orsay, France.
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12
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Szambowska A, Tessmer I, Prus P, Schlott B, Pospiech H, Grosse F. Cdc45-induced loading of human RPA onto single-stranded DNA. Nucleic Acids Res 2017; 45:3217-3230. [PMID: 28100698 PMCID: PMC5389570 DOI: 10.1093/nar/gkw1364] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 01/02/2017] [Indexed: 11/14/2022] Open
Abstract
Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8–10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork.
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Affiliation(s)
- Anna Szambowska
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, D-97080 Würzburg, Germany
| | - Piotr Prus
- Biocenter Oulu, P.O. Box 5000, 90014 University of Oulu, Finland
| | - Bernhard Schlott
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Proteomics Core Facility, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Helmut Pospiech
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Faculty of Biochemistry and Molecular Medicine, P.O. Box 5000, 90014 University of Oulu, Finland
| | - Frank Grosse
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Center for Molecular Biomedicine, Friedrich-Schiller University, Biochemistry Department, Jena, Germany
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13
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Krasikova YS, Rechkunova NI, Lavrik OI. Replication protein A as a major eukaryotic single-stranded DNA-binding protein and its role in DNA repair. Mol Biol 2016. [DOI: 10.1134/s0026893316030080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Safa L, Gueddouda NM, Thiébaut F, Delagoutte E, Petruseva I, Lavrik O, Mendoza O, Bourdoncle A, Alberti P, Riou JF, Saintomé C. 5' to 3' Unfolding Directionality of DNA Secondary Structures by Replication Protein A: G-QUADRUPLEXES AND DUPLEXES. J Biol Chem 2016; 291:21246-21256. [PMID: 27440048 DOI: 10.1074/jbc.m115.709667] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 11/06/2022] Open
Abstract
The replication protein A (RPA) is a single-stranded DNA-binding protein that plays an essential role in DNA metabolism. RPA is able to unfold G-quadruplex (G4) structures formed by telomeric DNA sequences, a function important for telomere maintenance. To elucidate the mechanism through which RPA unfolds telomeric G4s, we studied its interaction with oligonucleotides that adopt a G4 structure extended with a single-stranded tail on either side of the G4. Binding and unfolding was characterized using several biochemical and biophysical approaches and in the presence of specific G4 ligands, such as telomestatin and 360A. Our data show that RPA can bind on each side of the G4 but it unwinds the G4 only from 5' toward 3'. We explain the 5' to 3' unfolding directionality in terms of the 5' to 3' oriented laying out of hRPA subunits along single-stranded DNA. Furthermore, we demonstrate by kinetics experiments that RPA proceeds with the same directionality for duplex unfolding.
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Affiliation(s)
- Layal Safa
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France, the Sorbonne Universités, UPMC University Paris 06, F-75005, Paris, France
| | - Nassima Meriem Gueddouda
- the Laboratoire ARNA-INSERM U1212, UMR 5320, Institut européen de chimie et biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Frédéric Thiébaut
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France, the Sorbonne Universités, UPMC University Paris 06, F-75005, Paris, France, the Ecole Normale Supérieure, PSL Research University, Département de Chimie, 24 rue Lhomond, CNRS, UMR 7203 LBM, 75005 Paris, France, and
| | - Emmanuelle Delagoutte
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France
| | - Irina Petruseva
- the Novosibirsk Institute of Chemical Biology and Fundamental Medecine, Siberian Division of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Olga Lavrik
- the Novosibirsk Institute of Chemical Biology and Fundamental Medecine, Siberian Division of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Oscar Mendoza
- the Laboratoire ARNA-INSERM U1212, UMR 5320, Institut européen de chimie et biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Anne Bourdoncle
- the Laboratoire ARNA-INSERM U1212, UMR 5320, Institut européen de chimie et biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Patrizia Alberti
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France,
| | - Jean-François Riou
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France
| | - Carole Saintomé
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France, the Sorbonne Universités, UPMC University Paris 06, F-75005, Paris, France,
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15
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Abstract
XPA (xeroderma pigmentosum group A) protein is an essential factor for NER (nucleotide excision repair) which is believed to be involved in DNA damage recognition/verification, NER factor recruiting and stabilization of repair intermediates. Past studies on the structure of XPA have focused primarily on XPA interaction with damaged DNA. However, how XPA interacts with other DNA structures remains unknown though recent evidence suggest that these structures could be important for its roles in both NER and non-NER activities. Previously, we reported that XPA recognizes undamaged DNA ds/ssDNA (double-strand/single-strandDNA) junctions with a binding affinity much higher than its ability to bind bulky DNA damage. To understand how this interaction occurs biochemically we implemented a structural determination of the interaction using a MS-based protein footprinting method and limited proteolysis. By monitoring surface accessibility of XPA lysines to NHS-biotin modification in the free protein and the DNA junction-bound complex we show that XPA physically interacts with the DNA junctions via two lysines, K168 and K179, located in the previously known XPA(98–219) DBD (DNA-binding domain). Importantly, we also uncovered new lysine residues, outside of the known DBD, involved in the binding. We found that residues K221, K222, K224 and K236 in the C-terminal domain are involved in DNA binding. Limited proteolysis analysis of XPA–DNA interactions further confirmed this observation. Structural modelling with these data suggests a clamp-like DBD for the XPA binding to ds/ssDNA junctions. Our results provide a novel structure-function view of XPA–DNA junction interactions.
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16
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Maréchal A, Zou L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res 2014; 25:9-23. [PMID: 25403473 DOI: 10.1038/cr.2014.147] [Citation(s) in RCA: 313] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Replication Protein A (RPA) complex is an essential regulator of eukaryotic DNA metabolism. RPA avidly binds to single-stranded DNA (ssDNA) through multiple oligonucleotide/oligosaccharide-binding folds and coordinates the recruitment and exchange of genome maintenance factors to regulate DNA replication, recombination and repair. The RPA-ssDNA platform also constitutes a key physiological signal which activates the master ATR kinase to protect and repair stalled or collapsed replication forks during replication stress. In recent years, the RPA complex has emerged as a key target and an important regulator of post-translational modifications in response to DNA damage, which is critical for its genome guardian functions. Phosphorylation and SUMOylation of the RPA complex, and more recently RPA-regulated ubiquitination, have all been shown to control specific aspects of DNA damage signaling and repair by modulating the interactions between RPA and its partners. Here, we review our current understanding of the critical functions of the RPA-ssDNA platform in the maintenance of genome stability and its regulation through an elaborate network of covalent modifications.
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Affiliation(s)
- Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- 1] Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA [2] Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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17
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Safa L, Delagoutte E, Petruseva I, Alberti P, Lavrik O, Riou JF, Saintomé C. Binding polarity of RPA to telomeric sequences and influence of G-quadruplex stability. Biochimie 2014; 103:80-8. [PMID: 24747047 DOI: 10.1016/j.biochi.2014.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 04/09/2014] [Indexed: 01/01/2023]
Abstract
Replication protein A (RPA) is a single-stranded DNA binding protein that plays an essential role in telomere maintenance. RPA binds to and unfolds G-quadruplex (G4) structures formed in telomeric DNA, thus facilitating lagging strand DNA replication and telomerase activity. To investigate the effect of G4 stability on the interactions with human RPA (hRPA), we used a combination of biochemical and biophysical approaches. Our data revealed an inverse relationship between G4 stability and ability of hRPA to bind to telomeric DNA; notably small G4 ligands that enhance G4 stability strongly impaired G4 unfolding by hRPA. To gain more insight into the mechanism of binding and unfolding of telomeric G4 structures by RPA, we carried out photo-crosslinking experiments to elucidate the spatial arrangement of the RPA subunits along the DNA strands. Our results showed that RPA1 and RPA2 are arranged from 5' to 3' along the unfolded telomeric G4, as already described for unstructured single-stranded DNA, while no contact is possible with RPA3 on this short oligonucleotide. In addition, these data are compatible with a 5' to 3' directionality in G4 unfolding by hRPA.
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Affiliation(s)
- Layal Safa
- Structure des Acides Nucléiques, Télomères et Evolution, Inserm U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France; Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Emmanuelle Delagoutte
- Structure des Acides Nucléiques, Télomères et Evolution, Inserm U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Irina Petruseva
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Patrizia Alberti
- Structure des Acides Nucléiques, Télomères et Evolution, Inserm U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Olga Lavrik
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Jean-François Riou
- Structure des Acides Nucléiques, Télomères et Evolution, Inserm U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France.
| | - Carole Saintomé
- Structure des Acides Nucléiques, Télomères et Evolution, Inserm U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France; Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France.
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18
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Valton AL, Hassan-Zadeh V, Lema I, Boggetto N, Alberti P, Saintomé C, Riou JF, Prioleau MN. G4 motifs affect origin positioning and efficiency in two vertebrate replicators. EMBO J 2014; 33:732-46. [PMID: 24521668 DOI: 10.1002/embj.201387506] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA replication ensures the accurate duplication of the genome at each cell cycle. It begins at specific sites called replication origins. Genome-wide studies in vertebrates have recently identified a consensus G-rich motif potentially able to form G-quadruplexes (G4) in most replication origins. However, there is no experimental evidence to demonstrate that G4 are actually required for replication initiation. We show here, with two model origins, that G4 motifs are required for replication initiation. Two G4 motifs cooperate in one of our model origins. The other contains only one critical G4, and its orientation determines the precise position of the replication start site. Point mutations affecting the stability of this G4 in vitro also impair origin function. Finally, this G4 is not sufficient for origin activity and must cooperate with a 200-bp cis-regulatory element. In conclusion, our study strongly supports the predicted essential role of G4 in replication initiation.
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Affiliation(s)
- Anne-Laure Valton
- Institut Jacques Monod, CNRS UMR7592 Université Paris Diderot Equipe Labellisée Ligue contre le cancer, Paris, France
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19
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Fan J, Pavletich NP. Structure and conformational change of a replication protein A heterotrimer bound to ssDNA. Genes Dev 2012; 26:2337-47. [PMID: 23070815 DOI: 10.1101/gad.194787.112] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Replication protein A (RPA) is the main eukaryotic ssDNA-binding protein with essential roles in DNA replication, recombination, and repair. RPA maintains the DNA as single-stranded and also interacts with other DNA-processing proteins, coordinating their assembly and disassembly on DNA. RPA binds to ssDNA in two conformational states with opposing affinities for DNA and proteins. The RPA-protein interactions are compatible with a low DNA affinity state that involves DNA-binding domain A (DBD-A) and DBD-B but not with the high DNA affinity state that additionally engages DBD-C and DBD-D. The structure of the high-affinity RPA-ssDNA complex reported here shows a compact quaternary structure held together by a four-way interface between DBD-B, DBD-C, the intervening linker (BC linker), and ssDNA. The BC linker binds into the DNA-binding groove of DBD-B, mimicking DNA. The associated conformational change and partial occlusion of the DBD-A-DBA-B protein-protein interaction site establish a mechanism for the allosteric coupling of RPA-DNA and RPA-protein interactions.
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Affiliation(s)
- Jie Fan
- Sloan-Kettering Division, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA
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20
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Abstract
The human SSB homologue 1 (hSSB1) has been shown to facilitate homologous recombination and double-strand break signalling in human cells. Here, we compare the DNA-binding properties of the SOSS1 complex, containing SSB1, with Replication Protein A (RPA), the primary single-strand DNA (ssDNA) binding complex in eukaryotes. Ensemble and single-molecule approaches show that SOSS1 binds ssDNA with lower affinity compared to RPA, and exhibits less stable interactions with DNA substrates. Nevertheless, the SOSS1 complex is uniquely capable of promoting interaction of human Exo1 with double-strand DNA ends and stimulates its activity independently of the MRN complex in vitro. Both MRN and SOSS1 also act to mitigate the inhibitory action of the Ku70/80 heterodimer on Exo1 activity in vitro. These results may explain why SOSS complexes do not localize with RPA to replication sites in human cells, yet have a strong effect on double-strand break resection and homologous recombination.
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21
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22
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Prakash A, Borgstahl GEO. The structure and function of replication protein A in DNA replication. Subcell Biochem 2012; 62:171-96. [PMID: 22918586 DOI: 10.1007/978-94-007-4572-8_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In all organisms from bacteria and archaea to eukarya, single-stranded DNA binding proteins play an essential role in most, if not all, nuclear metabolism involving single-stranded DNA (ssDNA). Replication protein A (RPA), the major eukaryotic ssDNA binding protein, has two important roles in DNA metabolism: (1) in binding ssDNA to protect it and to keep it unfolded, and (2) in coordinating the assembly and disassembly of numerous proteins and protein complexes during processes such as DNA replication. Since its discovery as a vital player in the process of replication, RPAs roles in recombination and DNA repair quickly became evident. This chapter summarizes the current understanding of RPA's roles in replication by reviewing the available structural data, DNA-binding properties, interactions with various replication proteins, and interactions with DNA repair proteins when DNA replication is stalled.
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Affiliation(s)
- Aishwarya Prakash
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Given Medical Building, 89 Beaumont Avenue, Burlington, VT, 05405, USA
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23
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Carra C, Cucinotta FA. Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA. J Mol Model 2011; 18:2761-83. [PMID: 22116609 DOI: 10.1007/s00894-011-1288-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022]
Abstract
The eukaryotic replication protein A (RPA) has several pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Moreover, RPA seems to have a crucial role in organizing the sequential assembly of DNA processing proteins along single stranded DNA (ssDNA). The strong RPA affinity for ssDNA, K(A) between 10(-9)-10(-10) M, is characterized by a low cooperativity with minor variation for changes on the nucleotide sequence. Recently, new data on RPA interactions was reported, including the binding free energy of the complex RPA70AB with dC(8) and dC(5), which has been estimated to be -10 ± 0.4 kcal mol(-1) and -7 ± 1 kcal mol(-1), respectively. In view of these results we performed a study based on molecular dynamics aimed to reproduce the absolute binding free energy of RPA70AB with the dC(5) and dC(8) oligonucleotides. We used several tools to analyze the binding free energy, rigidity, and time evolution of the complex. The results obtained by MM-PBSA method, with the use of ligand free geometry as a reference for the receptor in the separate trajectory approach, are in excellent agreement with the experimental data, with ±4 kcal mol(-1) error. This result shows that the MM-PB(GB)SA methods can provide accurate quantitative estimates of the binding free energy for interacting complexes when appropriate geometries are used for the receptor, ligand and complex. The decomposition of the MM-GBSA energy for each residue in the receptor allowed us to correlate the change of the affinity of the mutated protein with the ΔG(gas+sol) contribution of the residue considered in the mutation. The agreement with experiment is optimal and a strong change in the binding free energy can be considered as the dominant factor in the loss for the binding affinity resulting from mutation.
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Affiliation(s)
- Claudio Carra
- Universities Space Research Association, Houston, TX 77058, USA.
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24
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Prakash A, Natarajan A, Marky LA, Ouellette MM, Borgstahl GEO. Identification of the DNA-Binding Domains of Human Replication Protein A That Recognize G-Quadruplex DNA. J Nucleic Acids 2011; 2011:896947. [PMID: 21772997 PMCID: PMC3136212 DOI: 10.4061/2011/896947] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 03/11/2011] [Indexed: 12/26/2022] Open
Abstract
Replication protein A (RPA), a key player in DNA metabolism, has 6 single-stranded DNA-(ssDNA-) binding domains (DBDs) A-F. SELEX experiments with the DBDs-C, -D, and -E retrieve a 20-nt G-quadruplex forming sequence. Binding studies show that RPA-DE binds preferentially to the G-quadruplex DNA, a unique preference not observed with other RPA constructs. Circular dichroism experiments show that RPA-CDE-core can unfold the G-quadruplex while RPA-DE stabilizes it. Binding studies show that RPA-C binds pyrimidine- and purine-rich sequences similarly. This difference between RPA-C and RPA-DE binding was also indicated by the inability of RPA-CDE-core to unfold an oligonucleotide containing a TC-region 5′ to the G-quadruplex. Molecular modeling studies of
RPA-DE and telomere-binding proteins Pot1 and Stn1 reveal structural similarities between the proteins and illuminate potential DNA-binding sites for RPA-DE and Stn1. These data indicate that DBDs of RPA have different ssDNA recognition properties.
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Affiliation(s)
- Aishwarya Prakash
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
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25
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Grimme JM, Spies M. FRET-based assays to monitor DNA binding and annealing by Rad52 recombination mediator protein. Methods Mol Biol 2011; 745:463-483. [PMID: 21660711 DOI: 10.1007/978-1-61779-129-1_27] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
During homologous recombination and homology-directed repair of broken chromosomes, proteins that mediate and oppose recombination form dynamic complexes on damaged DNA. Quantitative analysis of these nucleoprotein assemblies requires a robust signal, which reports on the association of a recombination mediator with its substrate and on the state of substrate DNA within the complex. Eukaryotic Rad52 protein mediates recombination, repair, and restart of collapsed replication forks by facilitating replacement of ssDNA binding protein replication protein A (RPA) with Rad51 recombinase and by mediating annealing of two complementary DNA strands protected by RPA. The characteristic binding mode whereby ssDNA is wrapped around the Rad52 ring allowed us to develop robust and sensitive FRET-based assays for monitoring Rad52 interactions with protein-free DNA and ssDNA-RPA complexes. By reporting on the configuration of ssDNA dually labeled with Cy3 and Cy5 fluorescent dyes, solution-based FRET is used to analyze Rad52-RPA-DNA interactions under equilibrium binding conditions. Finally, FRET between Cy3 and Cy5 dyes incorporated into two homologous ssDNA molecules can be used to analyze interplay between Rad52-mediated DNA strand annealing and duplex DNA destabilization by RPA.
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Affiliation(s)
- Jill M Grimme
- US Army Engineer Research Development Center, Construction Engineering Research Laboratory, Champaign, IL 61822, USA.
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26
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Richard DJ, Bolderson E, Khanna KK. Multiple human single-stranded DNA binding proteins function in genome maintenance: structural, biochemical and functional analysis. Crit Rev Biochem Mol Biol 2010; 44:98-116. [PMID: 19367476 DOI: 10.1080/10409230902849180] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two single-stranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein-protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.
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Affiliation(s)
- Derek J Richard
- Cancer and Cell Biology Division, The Queensland Institute of Medical Research, 300 Herston Road, Herston, QLD 4006, Australia
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27
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Grimme JM, Honda M, Wright R, Okuno Y, Rothenberg E, Mazin AV, Ha T, Spies M. Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes. Nucleic Acids Res 2010; 38:2917-30. [PMID: 20081207 PMCID: PMC2875008 DOI: 10.1093/nar/gkp1249] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Rad52 promotes the annealing of complementary strands of DNA bound by replication protein A (RPA) during discrete repair pathways. Here, we used a fluorescence resonance energy transfer (FRET) between two fluorescent dyes incorporated into DNA substrates to probe the mechanism by which human Rad52 (hRad52) interacts with and mediates annealing of ssDNA–hRPA complexes. Human Rad52 bound ssDNA or ssDNA–hRPA complex in two, concentration-dependent modes. At low hRad52 concentrations, ssDNA was wrapped around the circumference of the protein ring, while at higher protein concentrations, ssDNA was stretched between multiple hRad52 rings. Annealing by hRad52 occurred most efficiently when each complementary DNA strand or each ssDNA–hRPA complex was bound by hRad52 in a wrapped configuration, suggesting homology search and annealing occur via two hRad52–ssDNA complexes. In contrast to the wild type protein, hRad52RQK/AAA and hRad521–212 mutants with impaired ability to bind hRPA protein competed with hRPA for binding to ssDNA and failed to counteract hRPA-mediated duplex destabilization highlighting the importance of hRad52-hRPA interactions in promoting efficient DNA annealing.
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Affiliation(s)
- Jill M Grimme
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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28
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Broderick S, Rehmet K, Concannon C, Nasheuer HP. Eukaryotic single-stranded DNA binding proteins: central factors in genome stability. Subcell Biochem 2010; 50:143-163. [PMID: 20012581 DOI: 10.1007/978-90-481-3471-7_8] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The single-stranded DNA binding proteins (SSBs) are required to maintain the integrity of the genome in all organisms. Replication protein A (RPA) is a nuclear SSB protein found in all eukaryotes and is required for multiple processes in DNA metabolism such as DNA replication, DNA repair, DNA recombination, telomere maintenance and DNA damage signalling. RPA is a heterotrimeric complex, binds ssDNA with high affinity, and interacts specifically with multiple proteins to fulfil its function in eukaryotes. RPA is phosphorylated in a cell cycle and DNA damage-dependent manner with evidence suggesting that phosphorylation has an important function in modulating the cellular DNA damage response. Considering the DNA-binding properties of RPA a mechanism of "molecular counting" to initiate DNA damage-dependent signalling is discussed. Recently a human homologue to the RPA2 subunit, called RPA4, was discovered and RPA4 can substitute for RPA2 in the RPA complex resulting in an "alternative" RPA (aRPA), which can bind to ssDNA with similar affinity as canonical RPA. Additional human SSBs, hSSB1 and hSSB2, were recently identified, with hSSB1 being localized in the nucleus and having implications in DNA repair. Mitochondrial SSBs (mtSSBs) have been found in all eukaryotes studied. mtSSBs are related to prokaryotic SSBs and essential to main the genome stability in eukaryotic mitochondria. Recently human mtSSB was identified as a novel binding partner of p53 and that it is able to stimulate the intrinsic exonuclease activity of p53. These findings and recent results associated with mutations in RPA suggest a link of SSBs to cancer.
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Affiliation(s)
- Sandra Broderick
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
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29
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Nuss JE, Sweeney DJ, Alter GM. Prediction of and experimental support for the three-dimensional structure of replication protein A. Biochemistry 2009; 48:7892-905. [PMID: 19621872 DOI: 10.1021/bi801896s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replication protein A (RPA) is a heterotrimeric, multidomain, single-stranded DNA binding protein that is essential for DNA replication, repair, and recombination. Crystallographic and NMR studies on RPA protein fragments have provided structures for all domains; however, intact heterotrimeric RPA has resisted crystallization, and a complete protein structure has not yet been described. In this study, computational methods and experimental reactivity information (MRAN) were used to model the complete structure of RPA. To accomplish this, models of RPA's globular domains and its domain-linking regions were docked in various orders. We also determined rates of proteolytic cleavage and amino acid side chain chemical modifications in native, solution state RPA. These experimental data were used to select alternate modeling intermediates and final structural models, leading to a single model most consistent with our results. Using molecular dynamics simulations and multiple rounds of simulated annealing, we then relaxed this structural model and examined its flexibility. The family of resultant models is consistent with other, previously published, critical lines of evidence and with experimental reactivity data presented herein.
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Affiliation(s)
- Jonathan Eric Nuss
- Department of Biochemistry and Molecular Biology and Biomedical Sciences Ph.D. Program, Wright State University, Dayton, Ohio 45435, USA
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30
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Deng X, Prakash A, Dhar K, Baia GS, Kolar C, Oakley GG, Borgstahl GEO. Human replication protein A-Rad52-single-stranded DNA complex: stoichiometry and evidence for strand transfer regulation by phosphorylation. Biochemistry 2009; 48:6633-43. [PMID: 19530647 PMCID: PMC2710861 DOI: 10.1021/bi900564k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The eukaryotic single-stranded DNA-binding protein, replication protein A (RPA), is essential in DNA metabolism and is phosphorylated in response to DNA-damaging agents. Rad52 and RPA participate in the repair of double-stranded DNA breaks (DSBs). It is known that human RPA and Rad52 form a complex, but the molecular mass, stoichiometry, and exact role of this complex in DSB repair are unclear. In this study, absolute molecular masses of individual proteins and complexes were measured in solution using analytical size-exclusion chromatography coupled with multiangle light scattering, the protein species present in each purified fraction were verified via sodium dodecyl sulfate−polyacrylamide gel electrophoresis (SDS−PAGE)/Western analyses, and the presence of biotinylated ssDNA in the complexes was verified by chemiluminescence detection. Then, employing UV cross-linking, the protein partner holding the ssDNA was identified. These data show that phosphorylated RPA promoted formation of a complex with monomeric Rad52 and caused the transfer of ssDNA from RPA to Rad52. This suggests that RPA phosphorylation may regulate the first steps of DSB repair and is necessary for the mediator function of Rad52.
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Affiliation(s)
- Xiaoyi Deng
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 987696 Nebraska Medical Center, Omaha, Nebraska 68198-7696, USA
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31
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Pestryakov PE, Lavrik OI. Mechanisms of single-stranded DNA-binding protein functioning in cellular DNA metabolism. BIOCHEMISTRY (MOSCOW) 2009; 73:1388-404. [PMID: 19216707 DOI: 10.1134/s0006297908130026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review deals with analysis of mechanisms involved in coordination of DNA replication and repair by SSB proteins; characteristics of eukaryotic, prokaryotic, and archaeal SSB proteins are considered, which made it possible to distinguish general mechanisms specific for functioning of proteins from organisms of different life domains. Mechanisms of SSB protein interactions with DNA during metabolism of the latter are studied; structural organization of the SSB protein complexes with DNA, as well as structural and functional peculiarities of different SSB proteins are analyzed.
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Affiliation(s)
- P E Pestryakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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32
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Homologous recombinational repair factors are recruited and loaded onto the viral DNA genome in Epstein-Barr virus replication compartments. J Virol 2009; 83:6641-51. [PMID: 19386720 DOI: 10.1128/jvi.00049-09] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Homologous recombination is an important biological process that facilitates genome rearrangement and repair of DNA double-strand breaks (DSBs). The induction of Epstein-Barr virus (EBV) lytic replication induces ataxia telangiectasia-mutated (ATM)-dependent DNA damage checkpoint signaling, leading to the clustering of phosphorylated ATM and Mre11/Rad50/Nbs1 (MRN) complexes to sites of viral genome synthesis in nuclei. Here we report that homologous recombinational repair (HRR) factors such as replication protein A (RPA), Rad51, and Rad52 as well as MRN complexes are recruited and loaded onto the newly synthesized viral genome in replication compartments. The 32-kDa subunit of RPA is extensively phosphorylated at sites in accordance with those with ATM. The hyperphosphorylation of RPA32 causes a change in RPA conformation, resulting in a switch from the catalysis of DNA replication to the participation in DNA repair. The levels of Rad51 and phosphorylated RPA were found to increase with the progression of viral productive replication, while that of Rad52 proved constant. Furthermore, biochemical fractionation revealed increases in levels of DNA-bound forms of these HRRs. Bromodeoxyuridine-labeled chromatin immunoprecipitation and PCR analyses confirmed the loading of RPA, Rad 51, Rad52, and Mre11 onto newly synthesized viral DNA, and terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling analysis demonstrated DSBs in the EBV replication compartments. HRR factors might be recruited to repair DSBs on the viral genome in viral replication compartments. RNA interference knockdown of RPA32 and Rad51 prevented viral DNA synthesis remarkably, suggesting that homologous recombination and/or repair of viral DNA genome might occur, coupled with DNA replication to facilitate viral genome synthesis.
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33
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Dickson AM, Krasikova Y, Pestryakov P, Lavrik O, Wold MS. Essential functions of the 32 kDa subunit of yeast replication protein A. Nucleic Acids Res 2009; 37:2313-26. [PMID: 19244309 PMCID: PMC2673435 DOI: 10.1093/nar/gkp090] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Replication protein A (RPA) is a heterotrimeric (70, 32 and 14 kDa subunits), single-stranded DNA-binding protein required for cellular DNA metabolism. All subunits of RPA are essential for life, but the specific functions of the 32 and 14 kDa subunits remains unknown. The 32 kDa subunit (RPA2) has multiple domains, but only the central DNA-binding domain (called DBD D) is essential for life in Saccharomyces cerevisiae. To define the essential function(s) of RPA2 in S. cerevisiae, a series of site-directed mutant forms of DBD D were generated. These mutant constructs were then characterized in vitro and in vivo. The mutations had minimal effects on the overall structure and activity of the RPA complex. However, several mutants were shown to disrupt crosslinking of RPA2 to DNA and to dramatically lower the DNA-binding affinity of a RPA2-containing subcomplex. When introduced into S. cerevisiae, all DBD D mutants were viable and supported normal growth rates and DNA replication. These findings indicate that RPA2–DNA interactions are not essential for viability and growth in S. cerevisiae. We conclude that DNA-binding activity of RPA2 is dispensable in yeast and that the essential function of DBD D is intra- and/or inter-protein interactions.
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Affiliation(s)
- Anne M Dickson
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-2600, USA
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34
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Salas TR, Petruseva I, Lavrik O, Saintomé C. Evidence for direct contact between the RPA3 subunit of the human replication protein A and single-stranded DNA. Nucleic Acids Res 2008; 37:38-46. [PMID: 19010961 PMCID: PMC2615627 DOI: 10.1093/nar/gkn895] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Replication Protein A is a single-stranded (ss) DNA-binding protein that is highly conserved in eukaryotes and plays essential roles in many aspects of nucleic acid metabolism, including replication, recombination, DNA repair and telomere maintenance. It is a heterotrimeric complex consisting of three subunits: RPA1, RPA2 and RPA3. It possesses four DNA-binding domains (DBD), DBD-A, DBD-B and DBD-C in RPA1 and DBD-D in RPA2, and it binds ssDNA via a multistep pathway. Unlike the RPA1 and RPA2 subunits, no ssDNA-RPA3 interaction has as yet been observed although RPA3 contains a structural motif found in the other DBDs. We show here using 4-thiothymine residues as photoaffinity probe that RPA3 interacts directly with ssDNA on the 3'-side on a 31 nt ssDNA.
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Affiliation(s)
- Tonatiuh Romero Salas
- Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, CNRS-ParisVI-Paris XIII-UMR 7033, Paris, France
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35
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Binz SK, Wold MS. Regulatory functions of the N-terminal domain of the 70-kDa subunit of replication protein A (RPA). J Biol Chem 2008; 283:21559-70. [PMID: 18515800 PMCID: PMC2490791 DOI: 10.1074/jbc.m802450200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/22/2008] [Indexed: 01/07/2023] Open
Abstract
Replication protein A (RPA) is the major single-stranded DNA-binding protein in eukaryotes. RPA is composed of three subunits of 70, 32, and 14 kDa. The N-terminal domain of the 70-kDa subunit (RPA70) has weak DNA binding activity, interacts with proteins, and is involved in cellular DNA damage response. To define the mechanism by which this domain regulates RPA function, we analyzed the function of RPA forms containing a deletion of the N terminus of RPA70 and mutations in the phosphorylation domain of RPA (N-terminal 40 amino acids of the 32-kDa subunit). Although each individual mutation has only modest effects on RPA activity, a form combining both phosphorylation mimetic mutations and a deletion of the N-terminal domain of RPA70 was found to have dramatically altered activity. This combined mutant was defective in binding to short single-stranded DNA oligonucleotides and had altered interactions with proteins that bind to the DNA-binding core of RPA70. These results indicate that in the absence of the N-terminal domain of RPA70, a negatively charged phosphorylation domain disrupts the activity of the core DNA-binding domain of RPA. We conclude that the N-terminal domain of RPA70 functions by interacting with the phosphorylation domain of the 32-kDa subunit and blocking undesirable interactions with the core DNA-binding domain of RPA. These studies indicate that RPA conformation is important for regulating RPA-DNA and RPA-protein interactions.
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Affiliation(s)
- Sara K Binz
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52242-2600, USA
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36
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Mikhailov VS, Vanarsdall AL, Rohrmann GF. Isolation and characterization of the DNA-binding protein (DBP) of the Autographa californica multiple nucleopolyhedrovirus. Virology 2007; 370:415-29. [PMID: 17935748 DOI: 10.1016/j.virol.2007.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 08/29/2007] [Accepted: 09/05/2007] [Indexed: 11/24/2022]
Abstract
DNA-binding protein (DBP) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) was expressed as an N-terminal His(6)-tag fusion using a recombinant baculovirus and purified to near homogeneity. Purified DBP formed oligomers that were crosslinked by redox reagents resulting in predominantly protein dimers and tetramers. In gel retardation assays, DBP showed a high affinity for single-stranded oligonucleotides and was able to compete with another baculovirus SSB protein, LEF-3, for binding sites. DBP binding protected ssDNA against hydrolysis by a baculovirus alkaline nuclease AN/LEF-3 complex. Partial proteolysis by trypsin revealed a domain structure of DBP that is required for interaction with DNA and that can be disrupted by thermal treatment. Binding to ssDNA, but not to dsDNA, changed the pattern of proteolytic fragments of DBP indicating adjustments in protein structure upon interaction with ssDNA. DBP was capable of unwinding short DNA duplexes and also promoted the renaturation of long complementary strands of ssDNA into duplexes. The unwinding and renaturation activities of DBP, as well as the DNA binding activity, were sensitive to sulfhydryl reagents and were inhibited by oxidation of thiol groups with diamide or by alkylation with N-ethylmaleimide. A high affinity of DBP for ssDNA and its unwinding and renaturation activities confirmed identification of DBP as a member of the SSB/recombinase family. These activities and a tight association with subnuclear structures suggests that DBP is a component of the virogenic stroma that is involved in the processing of replicative intermediates.
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Affiliation(s)
- Victor S Mikhailov
- Department of Microbiology, Oregon State University, Corvallis, OR 97331-3804, USA.
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37
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Taneja P, Boche I, Hartmann H, Nasheuer HP, Grosse F, Fanning E, Weisshart K. Different activities of the largest subunit of replication protein A cooperate during SV40 DNA replication. FEBS Lett 2007; 581:3973-8. [PMID: 17673209 PMCID: PMC2045582 DOI: 10.1016/j.febslet.2007.07.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 07/06/2007] [Accepted: 07/16/2007] [Indexed: 11/23/2022]
Abstract
Replication protein A (RPA) is a stable heterotrimeric complex consisting of p70, p32 and p14 subunits. The protein plays a crucial role in SV40 minichromosome replication. Peptides of p70 representing interaction sites for the smaller two subunits, DNA as well as the viral initiator protein large T-antigen (Tag) and the cellular DNA polymerase alpha-primase (Pol) all interfered with the replication process indicating the importance of the different p70 activities in this process. Inhibition by the peptide disrupting protein-protein interactions was observed only during the pre-initiation stage prior to primer synthesis, suggesting the formation of a stable initiation complex between RPA, Tag and Pol at the primer end.
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Affiliation(s)
- Poonam Taneja
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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38
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Jiang X, Klimovich V, Arunkumar AI, Hysinger EB, Wang Y, Ott RD, Guler GD, Weiner B, Chazin WJ, Fanning E. Structural mechanism of RPA loading on DNA during activation of a simple pre-replication complex. EMBO J 2006; 25:5516-26. [PMID: 17110927 PMCID: PMC1679769 DOI: 10.1038/sj.emboj.7601432] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 10/19/2006] [Indexed: 11/09/2022] Open
Abstract
We report that during activation of the simian virus 40 (SV40) pre-replication complex, SV40 T antigen (Tag) helicase actively loads replication protein A (RPA) on emerging single-stranded DNA (ssDNA). This novel loading process requires physical interaction of Tag origin DNA-binding domain (OBD) with the RPA high-affinity ssDNA-binding domains (RPA70AB). Heteronuclear NMR chemical shift mapping revealed that Tag-OBD binds to RPA70AB at a site distal from the ssDNA-binding sites and that RPA70AB, Tag-OBD, and an 8-nucleotide ssDNA form a stable ternary complex. Intact RPA and Tag also interact stably in the presence of an 8-mer, but Tag dissociates from the complex when RPA binds to longer oligonucleotides. Together, our results imply that an allosteric change in RPA quaternary structure completes the loading reaction. A mechanistic model is proposed in which the ternary complex is a key intermediate that directly couples origin DNA unwinding to RPA loading on emerging ssDNA.
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Affiliation(s)
- Xiaohua Jiang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Vitaly Klimovich
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Alphonse I Arunkumar
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Erik B Hysinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Yingda Wang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Robert D Ott
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Gulfem D Guler
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Brian Weiner
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Departments of Biochemistry and Chemistry and Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725, USA. E-mail:
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Ctr., 1161 21st Avenue South, Nashville, TN 37232-8725, USA. Tel.: +1 615 343 5677; Fax: +1 615 343 6707; E-mail:
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39
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Salas TR, Petruseva I, Lavrik O, Bourdoncle A, Mergny JL, Favre A, Saintomé C. Human replication protein A unfolds telomeric G-quadruplexes. Nucleic Acids Res 2006; 34:4857-65. [PMID: 16973897 PMCID: PMC1635258 DOI: 10.1093/nar/gkl564] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G-quadruplex structures inhibit telomerase activity and must be disrupted for telomere elongation during S phase. It has been suggested that the replication protein A (RPA) could unwind and maintain single-stranded DNA in a state amenable to the binding of telomeric components. We show here that under near-physiological in vitro conditions, human RPA is able to bind and unfold G-quadruplex structures formed from a 21mer human telomeric sequence. Analyses by native gel electrophoresis, cross-linking and fluorescence resonance energy transfer indicate the formation of both 1:1 and 2:1 complexes in which G-quadruplexes are unfolded. In addition, quadruplex opening by hRPA is much faster than observed with the complementary DNA, demonstrating that this protein efficiently unfolds G-quartets. A two-step mechanism accounting for the binding of hRPA to G-quadruplexes is proposed. These data point to the involvement of hRPA in regulation of telomere maintenance.
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Affiliation(s)
| | - Irina Petruseva
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences630090 Novosibirsk, Russia
| | - Olga Lavrik
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences630090 Novosibirsk, Russia
| | - Anne Bourdoncle
- Laboratoire de Biophysique, INSERM U565, CNRS UMR 5153, Muséum National d'Histoire Naturelle USM 50343 rue Cuvier, 75005 Paris, France
| | - Jean-Louis Mergny
- Laboratoire de Biophysique, INSERM U565, CNRS UMR 5153, Muséum National d'Histoire Naturelle USM 50343 rue Cuvier, 75005 Paris, France
| | | | - Carole Saintomé
- To whom correspondence should be addressed. Tel: +33 1 44 27 40 86; Fax: +33 1 44 27 57 16;
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40
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Zou Y, Liu Y, Wu X, Shell SM. Functions of human replication protein A (RPA): from DNA replication to DNA damage and stress responses. J Cell Physiol 2006; 208:267-73. [PMID: 16523492 PMCID: PMC3107514 DOI: 10.1002/jcp.20622] [Citation(s) in RCA: 269] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Human replication protein A (RPA), a heterotrimeric protein complex, was originally defined as a eukaryotic single-stranded DNA binding (SSB) protein essential for the in vitro replication of simian virus 40 (SV40) DNA. Since then RPA has been found to be an indispensable player in almost all DNA metabolic pathways such as, but not limited to, DNA replication, DNA repair, recombination, cell cycle, and DNA damage checkpoints. Defects in these cellular reactions may lead to genome instability and, thus, the diseases with a high potential to evolve into cancer. This extensive involvement of RPA in various cellular activities implies a potential modulatory role for RPA in cellular responses to genotoxic insults. In support, RPA is hyperphosphorylated upon DNA damage or replication stress by checkpoint kinases including ataxia telangiectasia mutated (ATM), ATR (ATM and Rad3-related), and DNA-dependent protein kinase (DNA-PK). The hyperphosphorylation may change the functions of RPA and, thus, the activities of individual pathways in which it is involved. Indeed, there is growing evidence that hyperphosphorylation alters RPA-DNA and RPA-protein interactions. In addition, recent advances in understanding the molecular basis of the stress-induced modulation of RPA functions demonstrate that RPA undergoes a subtle structural change upon hyperphosphorylation, revealing a structure-based modulatory mechanism. Furthermore, given the crucial roles of RPA in a broad range of cellular processes, targeting RPA to inhibit its specific functions, particularly in DNA replication and repair, may serve a valuable strategy for drug development towards better cancer treatment.
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Affiliation(s)
- Yue Zou
- Department of Biochemistry and Molecular Biology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, USA.
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41
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Ghosh P, Moitra K, Maki N, Dey S. Allosteric modulation of the human P-glycoprotein involves conformational changes mimicking catalytic transition intermediates. Arch Biochem Biophys 2006; 450:100-12. [PMID: 16624245 DOI: 10.1016/j.abb.2006.02.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 02/21/2006] [Accepted: 02/23/2006] [Indexed: 10/24/2022]
Abstract
The drug transport function of human P-glycoprotein (Pgp, ABCB1) can be inhibited by a number of pharmacological agents collectively referred to as modulators or reversing agents. In this study, we demonstrate that certain thioxanthene-based Pgp modulators with an allosteric mode of action induce a distinct conformational change in the cytosolic domain of Pgp, which alters susceptibility to proteolytic digestion. Both cis and trans-isomers of the Pgp modulator flupentixol confer considerable protection of an 80 kDa Pgp fragment against trypsin digestion, that is recognized by a polyclonal antibody specific for the NH(2)-terminal half to Pgp. The protection by flupentixol is abolished in the Pgp F983A mutant that is impaired in modulation by flupentixols, indicating involvement of the allosteric site in generating the conformational change. A similar protection to an 80 kDa fragment is conferred by ATP, its nonhydrolyzable analog ATPgammaS, and by trapping of ADP-vanadate at the catalytic domain, but not by transport substrate vinblastine or by the competitive modulator cyclosporin A, suggesting different outcomes from modulator interaction at the allosteric site and at the substrate site. In summary, we demonstrate that allosteric interaction of flupentixols with Pgp generates conformational changes that mimic catalytic transition intermediates induced by nucleotide binding and hydrolysis, which may play a crucial role in allosteric inhibition of Pgp-mediated drug transport.
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Affiliation(s)
- Pratiti Ghosh
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, 4301 Jones Bridge Road, Bethesda, MD 20814-4799, USA
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42
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Mikhailov VS, Okano K, Rohrmann GF. Structural and functional analysis of the baculovirus single-stranded DNA-binding protein LEF-3. Virology 2006; 346:469-78. [PMID: 16375940 DOI: 10.1016/j.virol.2005.11.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 11/04/2005] [Accepted: 11/18/2005] [Indexed: 11/17/2022]
Abstract
The single-stranded DNA-binding protein LEF-3 of Autographa californica multinucleocapsid nucleopolyhedrovirus consists of 385 amino acid residues, forms oligomers, and promotes Mg2+-independent unwinding of DNA duplexes and annealing of complementary DNA strands. Partial proteolysis revealed that the DNA-binding domain of LEF-3 is located within a central region (residues 28 to 326) that is relatively resistant to proteolysis. In contrast, the N-terminus (27 residues) and C-terminal portion (59 residues) are not involved in interaction with DNA and are readily accessible to proteolytic digestion. Circular dichroism analyses showed that LEF-3 is a folded protein with an estimated alpha-helix content of more than 40%, but it is structurally unstable and undergoes unfolding in aqueous solutions at temperatures near 50 degrees C. Unfolding eliminated the LEF-3 domains that are resistant to proteolysis and randomized the digestion pattern by trypsin. The structural transition was irreversible and was accompanied by the generation of high molecular weight (MW) complexes. The thermal treatment inhibited DNA-binding and unwinding activity of LEF-3 but markedly stimulated its annealing activity. We propose that the shift in LEF-3 activities resulted from the generation of the high MW protein complexes, that specifically stimulate the annealing of complementary DNA strands by providing multiple DNA-binding sites and bringing into close proximity the interacting strands. The unfolded LEF-3 was active in a strand exchange reaction suggesting that it could be involved in the production of recombination intermediates.
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Affiliation(s)
- Victor S Mikhailov
- Department of Microbiology, Oregon State University, Nash Hall 220, Corvallis, OR 97331-3804, USA.
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43
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Liu Y, Kvaratskhelia M, Hess S, Qu Y, Zou Y. Modulation of replication protein A function by its hyperphosphorylation-induced conformational change involving DNA binding domain B. J Biol Chem 2005; 280:32775-83. [PMID: 16006651 PMCID: PMC1450107 DOI: 10.1074/jbc.m505705200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human replication protein A (RPA), composed of RPA70, RPA32, and RPA14 subunits, undergoes hyperphosphorylation in cells in response to DNA damage. Hyperphosphorylation that occurs predominately in the N-terminal region of RPA32 is believed to play a role in modulating the cellular activities of RPA essential for almost all DNA metabolic pathways. To understand how the hyperphosphorylation modulates the functions of RPA, we compared the structural characteristics of full-length native and hyperphosphorylated RPAs using mass spectrometric protein footprinting, fluorescence spectroscopy, and limited proteolysis. Our mass spectrometric data showed that of 24 lysines and 18 arginines readily susceptible to small chemical reagent modification in native RPA, the three residues Lys-343, Arg-335, and Arg-382, located in DNA binding domain B (DBD-B) of RPA70, were significantly shielded in the hyperphosphorylated protein. Tryptophan fluorescence studies indicated significant quenching of Trp-361, located in the DBD-B domain, induced by hyperphosphorylation of RPA. Consistently, DBD-B became more resistant to the limited proteolysis by chymotrypsin after RPA hyperphosphorylation. Taken together, our results indicate that upon hyperphosphorylation of RPA32 N terminus (RPA32N), RPA undergoes a conformational change involving the single-stranded DNA binding cleft of DBD-B. Comparison of the interactions of native and hyperphosphorylated RPAs with short single-stranded oligonucleotides or partial DNA duplexes with a short 5' or 3' single-stranded DNA tails showed reduced affinity for the latter protein. We propose that the hyperphosphorylation may play a role in modulating the cellular pathways by altering the DBD-B-mediated RPA-DNA and RPA-protein interactions, hypothetically via the interaction of hyperphosphorylated RPA32N with DBD-B.
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Affiliation(s)
- Yiyong Liu
- Department of Biochemistry and Molecular Biology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, USA
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44
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Mikhailov VS, Okano K, Rohrmann GF. The redox state of the baculovirus single-stranded DNA-binding protein LEF-3 regulates its DNA binding, unwinding, and annealing activities. J Biol Chem 2005; 280:29444-53. [PMID: 15944160 DOI: 10.1074/jbc.m503235200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The single-stranded (ss) DNA-binding protein LEF-3 of Autographa californica multinucleocapsid nucleopolyhedrovirus promoted Mg(2+)-independent unwinding of DNA duplexes and annealing of complementary DNA strands. The unwinding and annealing activities of LEF-3 appeared to act in a competitive manner and were determined by the ratio of protein to DNA. At subsaturating and saturating concentrations, LEF-3 promoted annealing, whereas it promoted unwinding at oversaturation of DNA substrates. The LEF-3 binding to ssDNA and unwinding activity were sensitive to redox agents and were inhibited by oxidation of thiol groups in LEF-3 with 1,1'-azobis(N,N-dimethylformamide) (diamide) or by modification with the thiol-conjugating agent N-ethylmaleimide. Both oxidation and alkylation increased the dissociation constant of the interaction with model oligonucleotides indicating a decrease in an intrinsic affinity of LEF-3 for ssDNA. These results proved that free thiol groups are essential both for LEF-3 interaction with ssDNA and for DNA unwinding. In contrast, oxidation or modification of thiol groups stimulated the annealing activity of LEF-3 partially due to suppression of its unwinding activity. Treatment of LEF-3 with the reducing agent dithiothreitol inhibited annealing, indicating association of this activity with the oxidized protein. Thus, the balance between annealing and unwinding activities of LEF-3 was determined by the redox state of protein with the oxidized state favoring annealing and the reduced state favoring unwinding. An LEF-3 mutant in which the conservative cysteine Cys(214) was replaced with serine showed both a decreased binding to DNA and a reduced unwinding activity, thus indicating that this residue might participate in the regulation of LEF-3 activities.
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Affiliation(s)
- Victor S Mikhailov
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804
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45
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Shell SM, Hess S, Kvaratskhelia M, Zou Y. Mass spectrometric identification of lysines involved in the interaction of human replication protein a with single-stranded DNA. Biochemistry 2005; 44:971-8. [PMID: 15654753 PMCID: PMC1450108 DOI: 10.1021/bi048208a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human replication protein A (hRPA), a heterotrimeric single-stranded DNA (ssDNA) binding protein, is required for many cellular pathways including DNA damage repair, recombination, and replication as well as the ATR-mediated DNA damage response. While extensive effort has been devoted to understanding the structural relationships between RPA and ssDNA, information is currently limited to the RPA domains, the trimerization core, and a partial cocrystal structure. In this work, we employed a mass spectrometric protein footprinting method of single amino acid resolution to investigate the interactions of the entire heterotrimeric hRPA with ssDNA. In particular, we monitored surface accessibility of RPA lysines with NHS-biotin modification in the contexts of the free protein and the nucleoprotein complex. Our results not only indicated excellent agreement with the available crystal structure data for RPA70 DBD-AB-ssDNA complex but also revealed new protein contacts in the nucleoprotein complex. In addition to two residues, K263 and K343 of p70, previously identified by cocrystallography as direct DNA contacts, we observed protection of five additional lysines (K183, K259, K489, K577, and K588 of p70) upon ssDNA binding to RPA. Three residues, K489, K577, and K588, are located in ssDNA binding domain C and are likely to establish the direct contacts with cognate DNA. In contrast, no ssDNA-contacting lysines were identified in DBD-D. In addition, two lysines, K183 and K259, are positioned outside the putative ssDNA binding cleft. We propose that the protection of these lysines could result from the RPA interdomain structural reorganization induced by ssDNA binding.
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Affiliation(s)
- Steven M Shell
- Department of Biochemistry and Molecular Biology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, USA
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46
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Nuss JE, Alter GM. Denaturation of replication protein A reveals an alternative conformation with intact domain structure and oligonucleotide binding activity. Protein Sci 2004; 13:1365-78. [PMID: 15096638 PMCID: PMC2286763 DOI: 10.1110/ps.04616304] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Replication protein A (RPA) is a heterotrimeric, multidomain, single-stranded DNA-binding protein. Using spectroscopic methods and methylene carbene-based chemical modification methods, we have identified conformational intermediates in the denaturation pathway of RPA. Intrinsic protein fluorescence studies reveal unfolding profiles composed of multiple transitions, with midpoints at 1.5, 2.7, 4.2, and 5.3 M urea. CD profiles of RPA unfolding are characterized by a single transition. RPA is stabilized with respect to the CD-monitored transition when bound to a dA15 oligonucleotide. However, oligonucleotide binding appears to exert little, if any, effect on the first fluorescence transition. Methylene carbene chemical modification, coupled with MALDI-TOF mass spectrometry analysis, was also used to monitor unfolding of several specific RPA folds of the protein. The unfolding profiles of the individual structures are characterized by single transitions similar to the CD-monitored transition. Each fold, however, unravels with different individual characteristics, suggesting significant autonomy. Based on results from chemical modification and spectroscopic analyses, we conclude the initial transition observed in fluorescence experiments represents a change in the juxtaposition of binding folds with little unraveling of the domain structures. The second transition represents the unfolding of the majority of fold structure, and the third transition observed by fluorescence correlates with the dissociation of the 70- and 32-kD subunits.
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Affiliation(s)
- Jonathan E Nuss
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio 45435-0001, USA
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47
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Binz SK, Sheehan AM, Wold MS. Replication Protein A phosphorylation and the cellular response to DNA damage. DNA Repair (Amst) 2004; 3:1015-24. [PMID: 15279788 DOI: 10.1016/j.dnarep.2004.03.028] [Citation(s) in RCA: 229] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Defects in cellular DNA metabolism have a direct role in many human disease processes. Impaired responses to DNA damage and basal DNA repair have been implicated as causal factors in diseases with DNA instability like cancer, Fragile X and Huntington's. Replication protein A (RPA) is essential for multiple processes in DNA metabolism including DNA replication, recombination and DNA repair pathways (including nucleotide excision, base excision and double-strand break repair). RPA is a single-stranded DNA-binding protein composed of subunits of 70-, 32- and 14-kDa. RPA binds ssDNA with high affinity and interacts specifically with multiple proteins. Cellular DNA damage causes the N-terminus of the 32-kDa subunit of human RPA to become hyper-phosphorylated. Current data indicates that hyper-phosphorylation causes a change in RPA conformation that down-regulates activity in DNA replication but does not affect DNA repair processes. This suggests that the role of RPA phosphorylation in the cellular response to DNA damage is to help regulate DNA metabolism and promote DNA repair.
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Affiliation(s)
- Sara K Binz
- Department of Biochemistry, University of Iowa Carver College of Medicine, 3107 MERF, Iowa City, IA 52242, USA
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48
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Apuzzo S, Abdelhakim A, Fortin AS, Gros P. Cross-talk between the paired domain and the homeodomain of Pax3: DNA binding by each domain causes a structural change in the other domain, supporting interdependence for DNA Binding. J Biol Chem 2004; 279:33601-12. [PMID: 15148315 DOI: 10.1074/jbc.m402949200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Pax3 protein has two DNA binding domains, a Paired domain (PD) and a paired-type Homeo domain (HD). Although the PD and HD can bind to cognate DNA sequences when expressed individually, genetic and biochemical data indicate that the two domains are functionally interdependent in intact Pax3. The mechanistic basis of this functional interdependence is unknown and was studied by protease sensitivity. Pax3 was modified by the creation of Factor Xa cleavage sites at discrete locations in the PD, the HD, and in the linker segment joining the PD and the HD (Xa172, Xa189, and Xa216) in individual Pax3 mutants. The effect of Factor Xa insertions on protein stability and on DNA binding by the PD and the HD was measured using specific target site sequences. Independent insertions at position 100 in the linker separating the first from the second helix-turn-helix motif of the PD and at position 216 immediately upstream of the HD were found to be readily accessible to Factor Xa cleavage. The effect of DNA binding by the PD or the HD on accessibility of Factor Xa sites inserted in the same or in the other domain was monitored and quantitated for multiple mutants bearing different numbers of Xa sites at each position. In general, DNA binding reduced accessibility of all sites, suggesting a more compact and less solvent-exposed structure of DNA-bound versus DNA-free Pax3. Results of dose response and time course experiments were consistent and showed that DNA binding by the PD not only caused a local structural change in the PD but also caused a conformational change in the HD (P3OPT binding to Xa216 mutants); similarly, DNA binding by the HD also caused a conformational change in the PD (P2 binding to Xa100 mutants). These results provide a structural basis for the functional interdependence of the two DNA binding domains of Pax3.
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Affiliation(s)
- Sergio Apuzzo
- Department of Biochemistry and McGill Cancer Center, McGill University, Quebec H1E 1S9, Canada.
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49
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Pestryakov PE, Khlimankov DY, Bochkareva E, Bochkarev A, Lavrik OI. Human replication protein A (RPA) binds a primer-template junction in the absence of its major ssDNA-binding domains. Nucleic Acids Res 2004; 32:1894-903. [PMID: 15047856 PMCID: PMC390355 DOI: 10.1093/nar/gkh346] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human nuclear single-stranded (ss) DNA- binding protein, replication protein A (RPA), is a heterotrimer consisting of three subunits: p70, p32 and p14. The protein-DNA interaction is mediated by several DNA-binding domains (DBDs): two major (A and B, also known as p70A and p70B) and several minor (C and D, also known as p70C and p32D, and, presumably, by p70N). Here, using crosslinking experiments, we investigated an interaction of RPA deletion mutants containing a subset of the DBDs with partial DNA duplexes containing 5'-protruding ssDNA tails of 10, 20 and 30 nt. The crosslinks were generated using either a 'zero-length' photoreactive group (4-thio-2'-deoxyuridine-5'-monophosphate) embedded in the 3' end of the DNA primer, or a group connected to the 3' end by a lengthy linker (5-[N-[N-(4-azido-2,5-difluoro-3- chloropyridine-6-yl)-3-aminopropionyl]-trans-3-aminopropenyl-1]-2'-deoxyuridine-5'-monophosphate). In the absence of two major DBDs, p70A and p70B, the RPA trimerization core (p70C.p32D.p14) was capable of correctly recognizing the primer- template junction and adopting an orientation similar to that in native RPA. Both p70C and p32D contributed to this recognition. However, the domain contribution differed depending on the size of the ssDNA. In contrast with the trimerization core, the RPA dimerization core (p32D.p14) was incapable of detectably recognizing the DNA- junction structures, suggesting an orchestrating role for p70C in this process.
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Affiliation(s)
- Pavel E Pestryakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Prospect Lavrentieva 8, 630090, Novosibirsk, Russia
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50
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Loo YM, Melendy T. Recruitment of replication protein A by the papillomavirus E1 protein and modulation by single-stranded DNA. J Virol 2004; 78:1605-15. [PMID: 14747526 PMCID: PMC369418 DOI: 10.1128/jvi.78.4.1605-1615.2004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the exception of viral proteins E1 and E2, papillomaviruses depend heavily on host replication machinery for replication of their viral genome. E1 and E2 are known to recruit many of the necessary cellular replication factors to the viral origin of replication. Previously, we reported a physical interaction between E1 and the major human single-stranded DNA (ssDNA)-binding protein, replication protein A (RPA). E1 was determined to bind to the 70-kDa subunit of RPA, RPA70. In this study, using E1-affinity coprecipitation and enzyme-linked immunosorbent assay-based interaction assays, we show that E1 interacts with the major ssDNA-binding domain of RPA. Consistent with our previous report, no measurable interaction between E1 and the two smaller subunits of RPA was detected. The interaction of E1 with RPA was substantially inhibited by ssDNA. The extent of this inhibition was dependent on the length of the DNA. A 31-nucleotide (nt) oligonucleotide strongly inhibited the E1-RPA interaction, while a 16-nt oligonucleotide showed an intermediate level of inhibition. In contrast, a 10-nt oligonucleotide showed no observable effect on the E1-RPA interaction. This inhibition was not dependent on the sequence of the DNA. Furthermore, ssDNA also inhibited the interaction of RPA with papillomavirus E2, simian virus 40 T antigen, human polymerase alpha-primase, and p53. Taken together, our results suggest a potential role for ssDNA in modulating RPA-protein interactions, in particular, the RPA-E1 interactions during papillomavirus DNA replication. A model for recruitment of RPA by E1 during papillomavirus DNA replication is proposed.
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Affiliation(s)
- Yueh-Ming Loo
- Department of Microbiology, and Witebsky Center for Microbial Pathogenesis and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
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