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Ding J, Li X, Shen J, Zhao Y, Zhong S, Lai L, Niu H, Qi Z. ssDNA accessibility of Rad51 is regulated by orchestrating multiple RPA dynamics. Nat Commun 2023; 14:3864. [PMID: 37391417 PMCID: PMC10313831 DOI: 10.1038/s41467-023-39579-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
The eukaryotic single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA) plays a crucial role in various DNA metabolic pathways, including DNA replication and repair, by dynamically associating with ssDNA. While the binding of a single RPA molecule to ssDNA has been thoroughly studied, the accessibility of ssDNA is largely governed by the bimolecular behavior of RPA, the biophysical nature of which remains unclear. In this study, we develop a three-step low-complexity ssDNA Curtains method, which, when combined with biochemical assays and a Markov chain model in non-equilibrium physics, allow us to decipher the dynamics of multiple RPA binding to long ssDNA. Interestingly, our results suggest that Rad52, the mediator protein, can modulate the ssDNA accessibility of Rad51, which is nucleated on RPA coated ssDNA through dynamic ssDNA exposure between neighboring RPA molecules. We find that this process is controlled by the shifting between the protection mode and action mode of RPA ssDNA binding, where tighter RPA spacing and lower ssDNA accessibility are favored under RPA protection mode, which can be facilitated by the Rfa2 WH domain and inhibited by Rad52 RPA interaction.
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Affiliation(s)
- Jiawei Ding
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, CA, USA
| | - Jiangchuan Shen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Yiling Zhao
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shuchen Zhong
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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Evdokimov AN, Tsidulko AY, Popov AV, Vorobiev YN, Lomzov AA, Koroleva LS, Silnikov VN, Petruseva IO, Lavrik OI. Structural basis for the recognition and processing of DNA containing bulky lesions by the mammalian nucleotide excision repair system. DNA Repair (Amst) 2018; 61:86-98. [DOI: 10.1016/j.dnarep.2017.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 11/30/2022]
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3
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Pokhrel N, Origanti S, Davenport EP, Gandhi D, Kaniecki K, Mehl RA, Greene EC, Dockendorff C, Antony E. Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids. Nucleic Acids Res 2017; 45:9413-9426. [PMID: 28934470 PMCID: PMC5766198 DOI: 10.1093/nar/gkx598] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/09/2017] [Indexed: 12/23/2022] Open
Abstract
An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance.
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Affiliation(s)
- Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Sofia Origanti
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | | | - Disha Gandhi
- Department of Chemistry, Marquette University, Milwaukee, WI 53201, USA
| | - Kyle Kaniecki
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Chris Dockendorff
- Department of Chemistry, Marquette University, Milwaukee, WI 53201, USA
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
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Ghospurkar PL, Wilson TM, Liu S, Herauf A, Steffes J, Mueller EN, Oakley GG, Haring SJ. Phosphorylation and cellular function of the human Rpa2 N-terminus in the budding yeast Saccharomyces cerevisiae. Exp Cell Res 2014; 331:183-199. [PMID: 25499885 DOI: 10.1016/j.yexcr.2014.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/29/2014] [Accepted: 12/02/2014] [Indexed: 11/18/2022]
Abstract
Maintenance of genome integrity is critical for proper cell growth. This occurs through accurate DNA replication and repair of DNA lesions. A key factor involved in both DNA replication and the DNA damage response is the heterotrimeric single-stranded DNA (ssDNA) binding complex Replication Protein A (RPA). Although the RPA complex appears to be structurally conserved throughout eukaryotes, the primary amino acid sequence of each subunit can vary considerably. Examination of sequence differences along with the functional interchangeability of orthologous RPA subunits or regions could provide insight into important regions and their functions. This might also allow for study in simpler systems. We determined that substitution of yeast Replication Factor A (RFA) with human RPA does not support yeast cell viability. Exchange of a single yeast RFA subunit with the corresponding human RPA subunit does not function due to lack of inter-species subunit interactions. Substitution of yeast Rfa2 with domains/regions of human Rpa2 important for Rpa2 function (i.e., the N-terminus and the loop 3-4 region) supports viability in yeast cells, and hybrid proteins containing human Rpa2 N-terminal phospho-mutations result in similar DNA damage phenotypes to analogous yeast Rfa2 N-terminal phospho-mutants. Finally, the human Rpa2 N-terminus (NT) fused to yeast Rfa2 is phosphorylated in a manner similar to human Rpa2 in human cells, indicating that conserved kinases recognize the human domain in yeast. The implication is that budding yeast represents a potential model system for studying not only human Rpa2 N-terminal phosphorylation, but also phosphorylation of Rpa2 N-termini from other eukaryotic organisms.
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Affiliation(s)
- Padmaja L Ghospurkar
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Timothy M Wilson
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Shengqin Liu
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Anna Herauf
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Jenna Steffes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Erica N Mueller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Gregory G Oakley
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Stuart J Haring
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA; Interdisciplinary Cellular and Molecular Biology Program, North Dakota State University, Fargo, ND 58108, USA.
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Gibb B, Ye LF, Gergoudis SC, Kwon Y, Niu H, Sung P, Greene EC. Concentration-dependent exchange of replication protein A on single-stranded DNA revealed by single-molecule imaging. PLoS One 2014; 9:e87922. [PMID: 24498402 PMCID: PMC3912175 DOI: 10.1371/journal.pone.0087922] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/31/2013] [Indexed: 11/18/2022] Open
Abstract
Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein necessary for all aspects of DNA metabolism involving an ssDNA intermediate, including DNA replication, repair, recombination, DNA damage response and checkpoint activation, and telomere maintenance [1], [2], [3]. The role of RPA in most of these reactions is to protect the ssDNA until it can be delivered to downstream enzymes. Therefore a crucial feature of RPA is that it must bind very tightly to ssDNA, but must also be easily displaced from ssDNA to allow other proteins to gain access to the substrate. Here we use total internal reflection fluorescence microscopy and nanofabricated DNA curtains to visualize the behavior of Saccharomyces cerevisiae RPA on individual strands of ssDNA in real-time. Our results show that RPA remains bound to ssDNA for long periods of time when free protein is absent from solution. In contrast, RPA rapidly dissociates from ssDNA when free RPA is present in solution allowing rapid exchange between the free and bound states. In addition, the S. cerevisiae DNA recombinase Rad51 and E. coli single-stranded binding protein (SSB) also promote removal of RPA from ssDNA. These results reveal an unanticipated exchange between bound and free RPA suggesting a binding mechanism that can confer exceptionally slow off rates, yet also enables rapid displacement through a direct exchange mechanism that is reliant upon the presence of free ssDNA-binding proteins in solution. Our results indicate that RPA undergoes constant microscopic dissociation under all conditions, but this is only manifested as macroscopic dissociation (i.e. exchange) when free proteins are present in solution, and this effect is due to mass action. We propose that the dissociation of RPA from ssDNA involves a partially dissociated intermediate, which exposes a small section of ssDNA allowing other proteins to access to the DNA.
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Affiliation(s)
- Bryan Gibb
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Ling F. Ye
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Stephanie C. Gergoudis
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- * E-mail:
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Abstract
Rfa2 is a ssDNA (single-stranded DNA)-binding protein that plays an important role in DNA replication, recombination and repair. Rfa2 is regulated by phosphorylation, which alters its protein–protein interaction and protein–DNA interaction. In the present study, we found that the Pph3–Psy2 phosphatase complex is responsible for Rfa2 dephosphorylation both during normal G1-phase and under DNA replication stress in Candida albicans. Phosphorylated Rfa2 extracted from pph3Δ or psy2Δ G1 cells exhibited diminished binding affinity to dsDNA (double-stranded DNA) but not to ssDNA. We also discovered that Cdc28 (cell division cycle 28) and Mec1 are responsible for Rfa2 phosphorylation in G1-phase and under DNA replication stress respectively. Moreover, MS revealed that the domain of Rfa2 that was phosphorylated in G1-phase differed from that phosphorylated under the stress conditions. The results of the present study imply that differential phosphorylation plays a crucial role in RPA (replication protein A) regulation.
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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: 20] [Impact Index Per Article: 1.7] [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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Abstract
Replication protein A (RPA), the major eukaryotic single-strand DNA (ssDNA)-binding protein, is essential for replication, repair, recombination, and checkpoint activation. Defects in RPA-associated cellular activities lead to genomic instability, a major factor in the pathogenesis of cancer and other diseases. ssDNA binding activity is primarily mediated by two domains in the 70-kDa subunit of the RPA complex. These ssDNA interactions are mediated by a combination of polar residues and four conserved aromatic residues. Mutation of the aromatic residues causes a modest decrease in binding to long (30-nucleotide) ssDNA fragments but results in checkpoint activation and cell cycle arrest in cells. We have used a combination of biochemical analysis and knockdown replacement studies in cells to determine the contribution of these aromatic residues to RPA function. Cells containing the aromatic residue mutants were able to progress normally through S-phase but were defective in DNA repair. Biochemical characterization revealed that mutation of the aromatic residues severely decreased binding to short ssDNA fragments less than 20 nucleotides long. These data indicate that altered binding of RPA to short ssDNA intermediates causes a defect in DNA repair but not in DNA replication. These studies show that cells require different RPA functions in DNA replication and DNA repair.
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Affiliation(s)
- Cathy S Hass
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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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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Haring SJ, Humphreys TD, Wold MS. A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression. Nucleic Acids Res 2009; 38:846-58. [PMID: 19942684 PMCID: PMC2817474 DOI: 10.1093/nar/gkp1062] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Replication Protein A (RPA) is a single-stranded DNA-binding protein essential for DNA replication, repair, recombination and cell-cycle regulation. A human homolog of the RPA2 subunit, called RPA4, was previously identified and shown to be expressed in colon mucosal and placental cells; however, the function of RPA4 was not determined. To examine the function of RPA4 in human cells, we carried out knockdown and replacement studies to determine whether RPA4 can substitute for RPA2 in the cell. Unlike RPA2, exogenous RPA4 expression did not support chromosomal DNA replication and lead to cell-cycle arrest in G2/M. In addition, RPA4 localized to sites of DNA repair and reduced γ-H2AX caused by RPA2 depletion. These studies suggest that RPA4 cannot support cell proliferation but can support processes that maintain the genomic integrity of the cell.
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Affiliation(s)
- Stuart J Haring
- Department of Biochemistry, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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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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