1
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Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Mirkin SM, Kim JC. Massive contractions of myotonic dystrophy type 2-associated CCTG tetranucleotide repeats occur via double-strand break repair with distinct requirements for DNA helicases. G3 (BETHESDA, MD.) 2024; 14:jkad257. [PMID: 37950892 PMCID: PMC10849350 DOI: 10.1093/g3journal/jkad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75 to 11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables the selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are involved in these massive contractions, indicating a mechanism that uses homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a short-track control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
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Affiliation(s)
- David Papp
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Luis A Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Theresa A Mai
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Terrance J Haanen
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Meghan A O’Donnell
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Ariel T Duran
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sophia M Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Jenni E Narvanto
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Berenice Arguello
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Marvin O Onwukwe
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
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2
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Adolph MB, Garje AS, Balakrishnan S, Morati F, Modesti M, Chazin WJ, Cortez D. CRISPR-dependent Base Editing Screens Identify Separation of Function Mutants of RADX with Altered RAD51 Regulatory Activity. J Mol Biol 2023; 435:168236. [PMID: 37572935 PMCID: PMC10530557 DOI: 10.1016/j.jmb.2023.168236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023]
Abstract
RAD51 forms nucleoprotein filaments to promote homologous recombination, replication fork reversal, and fork protection. Numerous factors regulate the stability of these filaments and improper regulation leads to genomic instability and ultimately disease including cancer. RADX is a single stranded DNA binding protein that modulates RAD51 filament stability. Here, we utilize a CRISPR-dependent base editing screen to tile mutations across RADX to delineate motifs required for RADX function. We identified separation of function mutants of RADX that bind DNA and RAD51 but have a reduced ability to stimulate its ATP hydrolysis activity. Cells expressing these RADX mutants accumulate RAD51 on chromatin, exhibit replication defects, have reduced growth, accumulate DNA damage, and are hypersensitive to DNA damage and replication stress. These results indicate that RADX must promote RAD51 ATP turnover to regulate RAD51 and genome stability during DNA replication.
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Affiliation(s)
- Madison B Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Atharv S Garje
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Swati Balakrishnan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Florian Morati
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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3
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Antoniuk-Majchrzak J, Enkhbaatar T, Długajczyk A, Kaminska J, Skoneczny M, Klionsky DJ, Skoneczna A. Stability of Rad51 recombinase and persistence of Rad51 DNA repair foci depends on post-translational modifiers, ubiquitin and SUMO. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119526. [PMID: 37364618 DOI: 10.1016/j.bbamcr.2023.119526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023]
Abstract
The DNA double-strand breaks are particularly deleterious, especially when an error-free repair pathway is unavailable, enforcing the error-prone recombination pathways to repair the lesion. Cells can resume the cell cycle but at the expense of decreased viability due to genome rearrangements. One of the major players involved in recombinational repair of DNA damage is Rad51 recombinase, a protein responsible for presynaptic complex formation. We previously showed that an increased level of this protein promotes the usage of illegitimate recombination. Here we show that the level of Rad51 is regulated via the ubiquitin-dependent proteolytic pathway. The ubiquitination of Rad51 depends on multiple E3 enzymes, including SUMO-targeted ubiquitin ligases. We also demonstrate that Rad51 can be modified by both ubiquitin and SUMO. Moreover, its modification with ubiquitin may lead to opposite effects: degradation dependent on Rad6, Rad18, Slx8, Dia2, and the anaphase-promoting complex, or stabilization dependent on Rsp5. We also show that post-translational modifications with SUMO and ubiquitin affect Rad51's ability to form and disassemble DNA repair foci, respectively, influencing cell cycle progression and cell viability in genotoxic stress conditions. Our data suggest the existence of a complex E3 ligases network that regulates Rad51 recombinase's turnover, its molecular activity, and access to DNA, limiting it to the proportions optimal for the actual cell cycle stage and growth conditions, e.g., stress. Dysregulation of this network would result in a drop in cell viability due to uncontrolled genome rearrangement in the yeast cells. In mammals would promote the development of genetic diseases and cancer.
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Affiliation(s)
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Anna Długajczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Daniel J Klionsky
- Life Sciences Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
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4
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Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Kolar K, Mirkin SM, Kim JC. Massive contractions of Myotonic Dystrophy Type 2-associated CCTG tetranucleotide repeats occur via double strand break repair with distinct requirements for helicases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548036. [PMID: 37461657 PMCID: PMC10350092 DOI: 10.1101/2023.07.06.548036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Myotonic Dystrophy Type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75-11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are required for these massive contractions, indicating a mechanism that involves homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a low-repeat control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kara Kolar
- Department of Biology, Tufts University, Medford, MA 02155
| | | | - Jane C. Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078
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5
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Abstract
AbstractIn B cells, IgD is expressed together with IgM through alternative splicing of primary VHDJH-Cμ-s-m-Cδ-s-m RNAs, and also through IgD class switch DNA recombination (CSR) via double-strand DNA breaks (DSB) and synapse of Sμ with σδ. How such DSBs are resolved is still unknown, despite our previous report showing that Rad52 effects the ‘short-range’ microhomology-mediated synapsis of intra-Sμ region DSBs. Here we find that induction of IgD CSR downregulates Zfp318, and promotes Rad52 phosphorylation and recruitment to Sμ and σδ, thereby leading to alternative end-joining (A-EJ)-mediated Sμ-σδ recombination with extensive microhomologies, VHDJH-Cδs transcription and sustained IgD secretion. Rad52 ablation in mouse Rad52−/− B cells aborts IgD CSR in vitro and in vivo and dampens the specific IgD antibody response to OVA. Rad52 knockdown in human B cells also abrogates IgD CSR. Finally, Rad52 phosphorylation is associated with high levels of IgD CSR and anti-nuclear IgD autoantibodies in patients with systemic lupus erythematosus and in lupus-prone mice. Our findings thus show that Rad52 mediates IgD CSR through microhomology-mediated A-EJ in concert with Zfp318 downregulation.
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6
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Meir A, Greene EC. Srs2 and Pif1 as Model Systems for Understanding Sf1a and Sf1b Helicase Structure and Function. Genes (Basel) 2021; 12:1319. [PMID: 34573298 PMCID: PMC8469786 DOI: 10.3390/genes12091319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/19/2023] Open
Abstract
Helicases are enzymes that convert the chemical energy stored in ATP into mechanical work, allowing them to move along and manipulate nucleic acids. The helicase superfamily 1 (Sf1) is one of the largest subgroups of helicases and they are required for a range of cellular activities across all domains of life. Sf1 helicases can be further subdivided into two classes called the Sf1a and Sf1b helicases, which move in opposite directions on nucleic acids. The results of this movement can range from the separation of strands within duplex nucleic acids to the physical remodeling or removal of nucleoprotein complexes. Here, we describe the characteristics of the Sf1a helicase Srs2 and the Sf1b helicase Pif1, both from the model organism Saccharomyces cerevisiae, focusing on the roles that they play in homologous recombination, a DNA repair pathway that is necessary for maintaining genome integrity.
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Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA;
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7
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Adolph MB, Mohamed TM, Balakrishnan S, Xue C, Morati F, Modesti M, Greene EC, Chazin WJ, Cortez D. RADX controls RAD51 filament dynamics to regulate replication fork stability. Mol Cell 2021; 81:1074-1083.e5. [PMID: 33453169 PMCID: PMC7935748 DOI: 10.1016/j.molcel.2020.12.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/02/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
The RAD51 recombinase forms nucleoprotein filaments to promote double-strand break repair, replication fork reversal, and fork stabilization. The stability of these filaments is highly regulated, as both too little and too much RAD51 activity can cause genome instability. RADX is a single-strand DNA (ssDNA) binding protein that regulates DNA replication. Here, we define its mechanism of action. We find that RADX inhibits RAD51 strand exchange and D-loop formation activities. RADX directly and selectively interacts with ATP-bound RAD51, stimulates ATP hydrolysis, and destabilizes RAD51 nucleofilaments. The RADX interaction with RAD51, in addition to its ssDNA binding capability, is required to maintain replication fork elongation rates and fork stability. Furthermore, BRCA2 can overcome the RADX-dependent RAD51 inhibition. Thus, RADX functions in opposition to BRCA2 in regulating RAD51 nucleofilament stability to ensure the right level of RAD51 function during DNA replication.
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Affiliation(s)
- Madison B Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Taha M Mohamed
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Swati Balakrishnan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Florian Morati
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université U105, Marseille, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université U105, Marseille, France
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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8
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Nguyen DD, Kim EY, Sang PB, Chai W. Roles of OB-Fold Proteins in Replication Stress. Front Cell Dev Biol 2020; 8:574466. [PMID: 33043007 PMCID: PMC7517361 DOI: 10.3389/fcell.2020.574466] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate DNA replication is essential for maintaining genome stability. However, this stability becomes vulnerable when replication fork progression is stalled or slowed - a condition known as replication stress. Prolonged fork stalling can cause DNA damage, leading to genome instabilities. Thus, cells have developed several pathways and a complex set of proteins to overcome the challenge at stalled replication forks. Oligonucleotide/oligosaccharide binding (OB)-fold containing proteins are a group of proteins that play a crucial role in fork protection and fork restart. These proteins bind to single-stranded DNA with high affinity and prevent premature annealing and unwanted nuclease digestion. Among these OB-fold containing proteins, the best studied in eukaryotic cells are replication protein A (RPA) and breast cancer susceptibility protein 2 (BRCA2). Recently, another RPA-like protein complex CTC1-STN1-TEN1 (CST) complex has been found to counter replication perturbation. In this review, we discuss the latest findings on how these OB-fold containing proteins (RPA, BRCA2, CST) cooperate to safeguard DNA replication and maintain genome stability.
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Affiliation(s)
| | | | | | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, United States
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9
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Ngo K, Epum EA, Friedman KL. Emerging non-canonical roles for the Rad51-Rad52 interaction in response to double-strand breaks in yeast. Curr Genet 2020; 66:917-926. [PMID: 32399607 DOI: 10.1007/s00294-020-01081-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022]
Abstract
DNA double-strand break repair allows cells to survive both exogenous and endogenous insults to the genome. In yeast, the recombinases Rad51 and Rad52 are central to multiple forms of homology-dependent repair. Classically, Rad51 and Rad52 are thought to act cooperatively, with formation of the functional Rad51 nucleofilament facilitated by the mediator function of Rad52. Several studies have now identified functions for the interaction between Rad51 and Rad52 that are independent of the mediator function of Rad52 and affect a seemingly diverse array of functions in de novo telomere addition, global chromosome mobility following DNA damage, Rad51 nucleofilament stability, checkpoint adaptation, and microhomology-mediated chromosome rearrangements. Here, we review these functions with an emphasis on our recent discovery that the Rad51-Rad52 interaction influences the probability of de novo telomere addition at sites preferentially targeted by telomerase following a double-strand break (DSB). We present data addressing the prevalence of sites within the yeast genome that are capable of stimulating de novo telomere addition following a DSB and speculate about the potential role such sites may play in genome stability.
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Affiliation(s)
- Katrina Ngo
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Esther A Epum
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
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10
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Epum EA, Mohan MJ, Ruppe NP, Friedman KL. Interaction of yeast Rad51 and Rad52 relieves Rad52-mediated inhibition of de novo telomere addition. PLoS Genet 2020; 16:e1008608. [PMID: 32012161 PMCID: PMC7018233 DOI: 10.1371/journal.pgen.1008608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/13/2020] [Accepted: 01/13/2020] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) are toxic forms of DNA damage that must be repaired to maintain genome integrity. Telomerase can act upon a DSB to create a de novo telomere, a process that interferes with normal repair and creates terminal deletions. We previously identified sequences in Saccharomyces cerevisiae (SiRTAs; Sites of Repair-associated Telomere Addition) that undergo unusually high frequencies of de novo telomere addition, even when the original chromosome break is several kilobases distal to the eventual site of telomerase action. Association of the single-stranded telomere binding protein Cdc13 with a SiRTA is required to stimulate de novo telomere addition. Because extensive resection must occur prior to Cdc13 binding, we utilized these sites to monitor the effect of proteins involved in homologous recombination. We find that telomere addition is significantly reduced in the absence of the Rad51 recombinase, while loss of Rad52, required for Rad51 nucleoprotein filament formation, has no effect. Deletion of RAD52 suppresses the defect of the rad51Δ strain, suggesting that Rad52 inhibits de novo telomere addition in the absence of Rad51. The ability of Rad51 to counteract this effect of Rad52 does not require DNA binding by Rad51, but does require interaction between the two proteins, while the inhibitory effect of Rad52 depends on its interaction with Replication Protein A (RPA). Intriguingly, the genetic interactions we report between RAD51 and RAD52 are similar to those previously observed in the context of checkpoint adaptation. Forced recruitment of Cdc13 fully restores telomere addition in the absence of Rad51, suggesting that Rad52, through its interaction with RPA-coated single-stranded DNA, inhibits the ability of Cdc13 to bind and stimulate telomere addition. Loss of the Rad51-Rad52 interaction also stimulates a subset of Rad52-dependent microhomology-mediated repair (MHMR) events, consistent with the known ability of Rad51 to prevent single-strand annealing. DNA double-strand breaks (DSBs) can lead to chromosome loss and rearrangement associated with cancer and genetic disease, so understanding how the cell coordinates multiple possible repair pathways is of critical importance. Telomerase is a ribonucleoprotein enzyme that uses an intrinsic RNA component as a template for the addition of highly repetitive, protective sequences (called telomeres) at normal chromosome ends. Rarely, telomerase acts upon a DSB to create a new or de novo telomere with resultant loss of sequences distal to the site of telomere addition. Here, we show that interactions between proteins with known roles during DSB repair modulate the probability of telomerase action at hotspots of de novo telomere addition in the yeast genome by influencing the association of Cdc13, a protein required for telomerase recruitment, with sites of telomere addition. Intriguingly, the same interactions that facilitate telomere addition prevent other types of rearrangements in response to chromosome breaks.
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Affiliation(s)
- Esther A. Epum
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Michael J. Mohan
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Nicholas P. Ruppe
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine L. Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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11
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Jenkins SS, Gore S, Guo X, Liu J, Ede C, Veaute X, Jinks-Robertson S, Kowalczykowski SC, Heyer WD. Role of the Srs2-Rad51 Interaction Domain in Crossover Control in Saccharomyces cerevisiae. Genetics 2019; 212:1133-1145. [PMID: 31142613 PMCID: PMC6707447 DOI: 10.1534/genetics.119.302337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 02/05/2023] Open
Abstract
Saccharomyces cerevisiae Srs2, in addition to its well-documented antirecombination activity, has been proposed to play a role in promoting synthesis-dependent strand annealing (SDSA). Here we report the identification and characterization of an SRS2 mutant with a single amino acid substitution (srs2-F891A) that specifically affects the Srs2 pro-SDSA function. This residue is located within the Srs2-Rad51 interaction domain and embedded within a protein sequence resembling a BRC repeat motif. The srs2-F891A mutation leads to a complete loss of interaction with Rad51 as measured through yeast two-hybrid analysis and a partial loss of interaction as determined through protein pull-down assays with purified Srs2, Srs2-F891A, and Rad51 proteins. Even though previous work has shown that internal deletions of the Srs2-Rad51 interaction domain block Srs2 antirecombination activity in vitro, the Srs2-F891A mutant protein, despite its weakened interaction with Rad51, exhibits no measurable defect in antirecombination activity in vitro or in vivo Surprisingly, srs2-F891A shows a robust shift from noncrossover to crossover repair products in a plasmid-based gap repair assay, but not in an ectopic physical recombination assay. Our findings suggest that the Srs2 C-terminal Rad51 interaction domain is more complex than previously thought, containing multiple interaction sites with unique effects on Srs2 activity.
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Affiliation(s)
- Shirin S Jenkins
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616
| | - Steven Gore
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616
| | - Xiaoge Guo
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616
| | - Christopher Ede
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616
| | - Xavier Veaute
- CEA, CIGEx, F-92265 Fontenay-aux-Roses Cedex, France
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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12
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Abstract
Homologous recombination (HR) is a universally conserved mechanism used to maintain genomic integrity. In eukaryotes, HR is used to repair the spontaneous double strand breaks (DSBs) that arise during mitotic growth, and the programmed DSBs that form during meiosis. The mechanisms that govern mitotic and meiotic HR share many similarities, however, there are also several key differences, which reflect the unique attributes of each process. For instance, even though many of the proteins involved in mitotic and meiotic HR are the same, DNA target specificity is not: mitotic DSBs are repaired primarily using the sister chromatid as a template, whereas meiotic DBSs are repaired primarily through targeting of the homologous chromosome. These changes in template specificity are induced by expression of meiosis-specific HR proteins, down-regulation of mitotic HR proteins, and the formation of meiosis-specific chromosomal structures. Here, we compare and contrast the biochemical properties of key recombination intermediates formed during the pre-synapsis phase of mitotic and meiotic HR. Throughout, we try to highlight unanswered questions that will shape our understanding of how homologous recombination contributes to human cancer biology and sexual reproduction.
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13
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The Main Role of Srs2 in DNA Repair Depends on Its Helicase Activity, Rather than on Its Interactions with PCNA or Rad51. mBio 2018; 9:mBio.01192-18. [PMID: 30018112 PMCID: PMC6050964 DOI: 10.1128/mbio.01192-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Homologous recombination (HR) is a mechanism that repairs a variety of DNA lesions. Under certain circumstances, however, HR can generate intermediates that can interfere with other cellular processes such as DNA transcription or replication. Cells have therefore developed pathways that abolish undesirable HR intermediates. The Saccharomyces cerevisiae yeast Srs2 helicase has a major role in one of these pathways. Srs2 also works during DNA replication and interacts with the clamp PCNA. The relative importance of Srs2’s helicase activity, Rad51 removal function, and PCNA interaction in genome stability remains unclear. We created a new SRS2 allele [srs2(1-850)] that lacks the whole C terminus, containing the interaction site for Rad51 and PCNA and interactions with many other proteins. Thus, the new allele encodes an Srs2 protein bearing only the activity of the DNA helicase. We find that the interactions of Srs2 with Rad51 and PCNA are dispensable for the main role of Srs2 in the repair of DNA damage in vegetative cells and for proper completion of meiosis. On the other hand, it has been shown that in cells impaired for the DNA damage tolerance (DDT) pathways, Srs2 generates toxic intermediates that lead to DNA damage sensitivity; we show that this negative Srs2 activity requires the C terminus of Srs2. Dissection of the genetic interactions of the srs2(1-850) allele suggest a role for Srs2’s helicase activity in sister chromatid cohesion. Our results also indicate that Srs2’s function becomes more central in diploid cells. Homologous recombination (HR) is a key mechanism that repairs damaged DNA. However, this process has to be tightly regulated; failure to regulate it can lead to genome instability. The Srs2 helicase is considered a regulator of HR; it was shown to be able to evict the recombinase Rad51 from DNA. Cells lacking Srs2 exhibit sensitivity to DNA-damaging agents, and in some cases, they display defects in DNA replication. The relative roles of the helicase and Rad51 removal activities of Srs2 in genome stability remain unclear. To address this question, we created a new Srs2 mutant which has only the DNA helicase domain. Our study shows that only the DNA helicase domain is needed to deal with DNA damage and assist in DNA replication during vegetative growth and in meiosis. Thus, our findings shift the view on the role of Srs2 in the maintenance of genome integrity.
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14
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Ma E, Dupaigne P, Maloisel L, Guerois R, Le Cam E, Coïc E. Rad52-Rad51 association is essential to protect Rad51 filaments against Srs2, but facultative for filament formation. eLife 2018; 7:32744. [PMID: 29985128 PMCID: PMC6056232 DOI: 10.7554/elife.32744] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/30/2018] [Indexed: 12/24/2022] Open
Abstract
Homology search and strand exchange mediated by Rad51 nucleoprotein filaments are key steps of the homologous recombination process. In budding yeast, Rad52 is the main mediator of Rad51 filament formation, thereby playing an essential role. The current model assumes that Rad51 filament formation requires the interaction between Rad52 and Rad51. However, we report here that Rad52 mutations that disrupt this interaction do not affect γ-ray- or HO endonuclease-induced gene conversion frequencies. In vivo and in vitro studies confirmed that Rad51 filaments formation is not affected by these mutations. Instead, we found that Rad52-Rad51 association makes Rad51 filaments toxic in Srs2-deficient cells after exposure to DNA damaging agents, independently of Rad52 role in Rad51 filament assembly. Importantly, we also demonstrated that Rad52 is essential for protecting Rad51 filaments against dissociation by the Srs2 DNA translocase. Our findings open new perspectives in the understanding of the role of Rad52 in eukaryotes.
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Affiliation(s)
- Emilie Ma
- DRF, IBFJ, iRCM, CEA, Fontenay-aux-Roses, France.,Université Paris-Saclay, Paris, France
| | - Pauline Dupaigne
- Université Paris-Saclay, Paris, France.,Signalisation, Noyaux et Innovation en Cancérologie, Institut Gustave Roussy, CNRS UMR 8126, Villejuif, France.,Université Paris-Sud, Orsay, France
| | - Laurent Maloisel
- DRF, IBFJ, iRCM, CEA, Fontenay-aux-Roses, France.,Université Paris-Saclay, Paris, France
| | - Raphaël Guerois
- Université Paris-Saclay, Paris, France.,Université Paris-Sud, Orsay, France.,DRF, i2BC, LBSR, CEA, Gif-sur-Yvette, France
| | - Eric Le Cam
- Université Paris-Saclay, Paris, France.,Signalisation, Noyaux et Innovation en Cancérologie, Institut Gustave Roussy, CNRS UMR 8126, Villejuif, France.,Université Paris-Sud, Orsay, France
| | - Eric Coïc
- DRF, IBFJ, iRCM, CEA, Fontenay-aux-Roses, France.,Université Paris-Saclay, Paris, France
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15
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Yeast Srs2 Helicase Promotes Redistribution of Single-Stranded DNA-Bound RPA and Rad52 in Homologous Recombination Regulation. Cell Rep 2018; 21:570-577. [PMID: 29045827 DOI: 10.1016/j.celrep.2017.09.073] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/06/2017] [Accepted: 09/22/2017] [Indexed: 12/20/2022] Open
Abstract
Srs2 is a super-family 1 helicase that promotes genome stability by dismantling toxic DNA recombination intermediates. However, the mechanisms by which Srs2 remodels or resolves recombination intermediates remain poorly understood. Here, single-molecule imaging is used to visualize Srs2 in real time as it acts on single-stranded DNA (ssDNA) bound by protein factors that function in recombination. We demonstrate that Srs2 is highly processive and translocates rapidly (∼170 nt per second) in the 3'→5' direction along ssDNA saturated with replication protein A (RPA). We show that RPA is evicted from DNA during the passage of Srs2. Remarkably, Srs2 also readily removes the recombination mediator Rad52 from RPA-ssDNA and, in doing so, promotes rapid redistribution of both Rad52 and RPA. These findings have important mechanistic implications for understanding how Srs2 and related nucleic acid motor proteins resolve potentially pathogenic nucleoprotein intermediates.
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16
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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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17
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Niu H, Klein HL. Multifunctional roles of Saccharomyces cerevisiae Srs2 protein in replication, recombination and repair. FEMS Yeast Res 2017; 17:fow111. [PMID: 28011904 DOI: 10.1093/femsyr/fow111] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/22/2016] [Indexed: 11/12/2022] Open
Abstract
The Saccharomyces cerevisiae Srs2 DNA helicase has important roles in DNA replication, recombination and repair. In replication, Srs2 aids in repair of gaps by repair synthesis by preventing gaps from being used to initiate recombination. This is considered to be an anti-recombination role. In recombination, Srs2 plays both prorecombination and anti-recombination roles to promote the synthesis-dependent strand annealing recombination pathway and to inhibit gaps from initiating homologous recombination. In repair, the Srs2 helicase actively promotes gap repair through an interaction with the Exo1 nuclease to enlarge a gap for repair and to prevent Rad51 protein from accumulating on single-stranded DNA. Finally, Srs2 helicase can unwind hairpin-forming repeat sequences to promote replication and prevent repeat instability. The Srs2 activities can be controlled by phosphorylation, SUMO modification and interaction with key partners at DNA damage or lesions sites, which include PCNA and Rad51. These interactions can also limit DNA polymerase function during recombinational repair independent of the Srs2 translocase or helicase activity, further highlighting the importance of the Srs2 protein in regulating recombination. Here we review the myriad roles of Srs2 that have been documented in genome maintenance and distinguish between the translocase, helicase and additional functions of the Srs2 protein.
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Affiliation(s)
- Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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18
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Liu J, Ede C, Wright WD, Gore SK, Jenkins SS, Freudenthal BD, Todd Washington M, Veaute X, Heyer WD. Srs2 promotes synthesis-dependent strand annealing by disrupting DNA polymerase δ-extending D-loops. eLife 2017; 6. [PMID: 28535142 PMCID: PMC5441872 DOI: 10.7554/elife.22195] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 04/29/2017] [Indexed: 01/12/2023] Open
Abstract
Synthesis-dependent strand annealing (SDSA) is the preferred mode of homologous recombination in somatic cells leading to an obligatory non-crossover outcome, thus avoiding the potential for chromosomal rearrangements and loss of heterozygosity. Genetic analysis identified the Srs2 helicase as a prime candidate to promote SDSA. Here, we demonstrate that Srs2 disrupts D-loops in an ATP-dependent fashion and with a distinct polarity. Specifically, we partly reconstitute the SDSA pathway using Rad51, Rad54, RPA, RFC, DNA Polymerase δ with different forms of PCNA. Consistent with genetic data showing the requirement for SUMO and PCNA binding for the SDSA role of Srs2, Srs2 displays a slight but significant preference to disrupt extending D-loops over unextended D-loops when SUMOylated PCNA is present, compared to unmodified PCNA or monoubiquitinated PCNA. Our data establish a biochemical mechanism for the role of Srs2 in crossover suppression by promoting SDSA through disruption of extended D-loops. DOI:http://dx.doi.org/10.7554/eLife.22195.001
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Affiliation(s)
- Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Christopher Ede
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - William D Wright
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Steven K Gore
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Shirin S Jenkins
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Bret D Freudenthal
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, United States
| | - M Todd Washington
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, United States
| | | | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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19
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Remodeling and Control of Homologous Recombination by DNA Helicases and Translocases that Target Recombinases and Synapsis. Genes (Basel) 2016; 7:genes7080052. [PMID: 27548227 PMCID: PMC4999840 DOI: 10.3390/genes7080052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/24/2016] [Accepted: 08/12/2016] [Indexed: 11/16/2022] Open
Abstract
Recombinase enzymes catalyse invasion of single-stranded DNA (ssDNA) into homologous duplex DNA forming "Displacement loops" (D-loops), a process called synapsis. This triggers homologous recombination (HR), which can follow several possible paths to underpin DNA repair and restart of blocked and collapsed DNA replication forks. Therefore, synapsis can be a checkpoint for controlling whether or not, how far, and by which pathway, HR proceeds to overcome an obstacle or break in a replication fork. Synapsis can be antagonized by limiting access of a recombinase to ssDNA and by dissociation of D-loops or heteroduplex formed by synapsis. Antagonists include DNA helicases and translocases that are identifiable in eukaryotes, bacteria and archaea, and which target synaptic and pre-synaptic DNA structures thereby controlling HR at early stages. Here we survey these events with emphasis on enabling DNA replication to be resumed from sites of blockage or collapse. We also note how knowledge of anti-recombination activities could be useful to improve efficiency of CRISPR-based genome editing.
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20
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Foertsch F, Szambowska A, Weise A, Zielinski A, Schlott B, Kraft F, Mrasek K, Borgmann K, Pospiech H, Grosse F, Melle C. S100A11 plays a role in homologous recombination and genome maintenance by influencing the persistence of RAD51 in DNA repair foci. Cell Cycle 2016; 15:2766-79. [PMID: 27590262 DOI: 10.1080/15384101.2016.1220457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is an essential process in maintenance of chromosomal stability. A key player of HR is the strand exchange factor RAD51 whose assembly at sites of DNA damage is tightly regulated. We detected an endogenous complex of RAD51 with the calcium-binding protein S100A11, which is localized at sites of DNA repair in HaCaT cells as well as in normal human epidermal keratinocytes (NHEK) synchronized in S phase. In biochemical assays, we revealed that S100A11 enhanced the RAD51 strand exchange activity. When cells expressing a S100A11 mutant lacking the ability to bind Ca(2+), a prolonged persistence of RAD51 in repair sites and nuclear γH2AX foci was observed suggesting an incomplete DNA repair. The same phenotype became apparent when S100A11 was depleted by RNA interference. Furthermore, down-regulation of S100A11 resulted in both reduced sister chromatid exchange confirming the restriction of the recombination capacity of the cells, and in an increase of chromosomal aberrations reflecting the functional requirement of S100A11 for the maintenance of genomic stability. Our data indicate that S100A11 is involved in homologous recombination by regulating the appearance of RAD51 in DSB repair sites. This function requires the calcium-binding activity of S100A11.
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Affiliation(s)
- Franziska Foertsch
- a Biomolecular Photonics Group , Jena University Hospital , Jena , Germany
| | - Anna Szambowska
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany
| | - Anja Weise
- c Institute of Human Genetics , Jena University Hospital , Jena , Germany
| | - Alexandra Zielinski
- d Radiobiology & Experimental Radiooncology , University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Bernhard Schlott
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany
| | - Florian Kraft
- c Institute of Human Genetics , Jena University Hospital , Jena , Germany
| | - Kristin Mrasek
- c Institute of Human Genetics , Jena University Hospital , Jena , Germany
| | - Kerstin Borgmann
- d Radiobiology & Experimental Radiooncology , University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Helmut Pospiech
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany.,e Faculty of Biochemistry and Molecular Medicine , University of Oulu , Finland
| | - Frank Grosse
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany
| | - Christian Melle
- a Biomolecular Photonics Group , Jena University Hospital , Jena , Germany
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21
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Silva S, Altmannova V, Eckert-Boulet N, Kolesar P, Gallina I, Hang L, Chung I, Arneric M, Zhao X, Buron LD, Mortensen UH, Krejci L, Lisby M. SUMOylation of Rad52-Rad59 synergistically change the outcome of mitotic recombination. DNA Repair (Amst) 2016; 42:11-25. [PMID: 27130983 DOI: 10.1016/j.dnarep.2016.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022]
Abstract
Homologous recombination (HR) is essential for maintenance of genome stability through double-strand break (DSB) repair, but at the same time HR can lead to loss of heterozygosity and uncontrolled recombination can be genotoxic. The post-translational modification by SUMO (small ubiquitin-like modifier) has been shown to modulate recombination, but the exact mechanism of this regulation remains unclear. Here we show that SUMOylation stabilizes the interaction between the recombination mediator Rad52 and its paralogue Rad59 in Saccharomyces cerevisiae. Although Rad59 SUMOylation is not required for survival after genotoxic stress, it affects the outcome of recombination to promote conservative DNA repair. In some genetic assays, Rad52 and Rad59 SUMOylation act synergistically. Collectively, our data indicate that the described SUMO modifications affect the balance between conservative and non-conservative mechanisms of HR.
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Affiliation(s)
- Sonia Silva
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Veronika Altmannova
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic
| | - Nadine Eckert-Boulet
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter Kolesar
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic
| | - Irene Gallina
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Lisa Hang
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Inn Chung
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Milica Arneric
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Line Due Buron
- Department of Systems Biology, Technical University of Denmark, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Systems Biology, Technical University of Denmark, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, Brno 625 00, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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22
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Xu X, Blackwell S, Lin A, Li F, Qin Z, Xiao W. Error-free DNA-damage tolerance in Saccharomyces cerevisiae. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 764:43-50. [DOI: 10.1016/j.mrrev.2015.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/07/2015] [Accepted: 02/06/2015] [Indexed: 12/18/2022]
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23
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DNA Double-Strand Break Repair Inhibitors as Cancer Therapeutics. ACTA ACUST UNITED AC 2015; 22:17-29. [DOI: 10.1016/j.chembiol.2014.11.013] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/26/2014] [Accepted: 11/10/2014] [Indexed: 12/29/2022]
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24
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Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms. Nature 2014; 511:251-4. [PMID: 24896181 PMCID: PMC4140095 DOI: 10.1038/nature13292] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/28/2014] [Indexed: 11/09/2022]
Abstract
Srs2 helicase is known to dismantle nucleofilaments of Rad51 recombinase to prevent spurious recombination events and unwind trinucleotide sequences that are prone to hairpin formation. Here we document a new, unexpected genome maintenance role of Srs2 in the suppression of mutations arising from mis-insertion of ribonucleoside monophosphates during DNA replication. In cells lacking RNase H2, Srs2 unwinds DNA from the 5' side of a nick generated by DNA topoisomerase I at a ribonucleoside monophosphate residue. In addition, Srs2 interacts with and enhances the activity of the nuclease Exo1, to generate a DNA gap in preparation for repair. Srs2-Exo1 thus functions in a new pathway of nick processing-gap filling that mediates tolerance of ribonucleoside monophosphates in the genome. Our results have implications for understanding the basis of Aicardi-Goutières syndrome, which stems from inactivation of the human RNase H2 complex.
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25
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Qiu Y, Antony E, Doganay S, Koh HR, Lohman TM, Myong S. Srs2 prevents Rad51 filament formation by repetitive motion on DNA. Nat Commun 2014; 4:2281. [PMID: 23939144 DOI: 10.1038/ncomms3281] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/09/2013] [Indexed: 11/09/2022] Open
Abstract
Srs2 dismantles presynaptic Rad51 filaments and prevents its re-formation as an anti-recombinase. However, the molecular mechanism by which Srs2 accomplishes these tasks remains unclear. Here we report a single-molecule fluorescence study of the dynamics of Rad51 filament formation and its disruption by Srs2. Rad51 forms filaments on single-stranded DNA by sequential binding of primarily monomers and dimers in a 5'-3' direction. One Rad51 molecule binds to three nucleotides, and six monomers are required to achieve a stable nucleation cluster. Srs2 exhibits ATP-dependent repetitive motion on single-stranded DNA and this activity prevents re-formation of the Rad51 filament. The same activity of Srs2 cannot prevent RecA filament formation, indicating its specificity for Rad51. Srs2's DNA-unwinding activity is greatly suppressed when Rad51 filaments form on duplex DNA. Taken together, our results reveal an exquisite and highly specific mechanism by which Srs2 regulates the Rad51 filament formation.
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Affiliation(s)
- Yupeng Qiu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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26
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Godin S, Wier A, Kabbinavar F, Bratton-Palmer DS, Ghodke H, Van Houten B, VanDemark AP, Bernstein KA. The Shu complex interacts with Rad51 through the Rad51 paralogues Rad55-Rad57 to mediate error-free recombination. Nucleic Acids Res 2013; 41:4525-34. [PMID: 23460207 PMCID: PMC3632125 DOI: 10.1093/nar/gkt138] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Saccharomyces cerevisiae Shu complex, consisting of Shu1, Shu2, Csm2 and Psy3, promotes error-free homologous recombination (HR) by an unknown mechanism. Recent structural analysis of two Shu proteins, Csm2 and Psy3, has revealed that these proteins are Rad51 paralogues and mediate DNA binding of this complex. We show in vitro that the Csm2–Psy3 heterodimer preferentially binds synthetic forked DNA or 3′-DNA overhang substrates resembling structures used during HR in vivo. We find that Csm2 interacts with Rad51 and the Rad51 paralogues, the Rad55–Rad57 heterodimer and that the Shu complex functions in the same epistasis group as Rad55–Rad57. Importantly, Csm2’s interaction with Rad51 is dependent on Rad55, whereas Csm2’s interaction with Rad55 occurs independently of Rad51. Consistent with the Shu complex containing Rad51 paralogues, the methyl methanesulphonate sensitivity of Csm2 is exacerbated at colder temperatures. Furthermore, Csm2 and Psy3 are needed for efficient recruitment of Rad55 to DNA repair foci after DNA damage. Finally, we observe that the Shu complex preferentially promotes Rad51-dependent homologous recombination over Rad51-independent repair. Our data suggest a model in which Csm2–Psy3 recruit the Shu complex to HR substrates, where it interacts with Rad51 through Rad55–Rad57 to stimulate Rad51 filament assembly and stability, promoting error-free repair.
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Affiliation(s)
- Stephen Godin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
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27
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Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis. EMBO J 2013; 32:742-55. [PMID: 23395907 PMCID: PMC3594751 DOI: 10.1038/emboj.2013.9] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 01/10/2013] [Indexed: 12/11/2022] Open
Abstract
Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. An unexpected non-catalytic function of the recombination-attenuating helicase Srs2 further expands the manifold roles of PCNA modifications in ensuring genome stability.
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Marini V, Krejci L. Unwinding of synthetic replication and recombination substrates by Srs2. DNA Repair (Amst) 2012; 11:789-98. [PMID: 22921573 PMCID: PMC3484393 DOI: 10.1016/j.dnarep.2012.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/14/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022]
Abstract
The budding yeast Srs2 protein possesses 3′ to 5′ DNA helicase activity and channels untimely recombination to post-replication repair by removing Rad51 from ssDNA. However, it also promotes recombination via a synthesis-dependent strand-annealing pathway (SDSA). Furthermore, at the replication fork, Srs2 is required for fork progression and prevents the instability of trinucleotide repeats. To better understand the multiple roles of the Srs2 helicase during these processes, we analysed the ability of Srs2 to bind and unwind various DNA substrates that mimic structures present during DNA replication and recombination. While leading or lagging strands were efficiently unwound, the presence of ssDNA binding protein RPA presented an obstacle for Srs2 translocation. We also tested the preferred directionality of unwinding of various substrates and studied the effect of Rad51 and Mre11 proteins on Srs2 helicase activity. These biochemical results help us understand the possible role of Srs2 in the processing of stalled or blocked replication forks as a part of post-replication repair as well as homologous recombination (HR).
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Affiliation(s)
- Victoria Marini
- Department of Biology, Masaryk University, Kamenice, Brno, Czech Republic
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29
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Karpenshif Y, Bernstein KA. From yeast to mammals: recent advances in genetic control of homologous recombination. DNA Repair (Amst) 2012; 11:781-8. [PMID: 22889934 DOI: 10.1016/j.dnarep.2012.07.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 11/26/2022]
Abstract
Misregulation of DNA repair is associated with genetic instability and tumorigenesis. To preserve the integrity of the genome, eukaryotic cells have evolved extremely intricate mechanisms for repairing DNA damage. One type of DNA lesion is a double-strand break (DSB), which is highly toxic when unrepaired. Repair of DSBs can occur through multiple mechanisms. Aside from religating the DNA ends, a homologous template can be used for repair in a process called homologous recombination (HR). One key step in committing to HR is the formation of Rad51 filaments, which perform the homology search and strand invasion steps. In S. cerevisiae, Srs2 is a key regulator of Rad51 filament formation and disassembly. In this review, we highlight potential candidates of Srs2 orthologues in human cells, and we discuss recent advances in understanding how Srs2's so-called "anti-recombinase" activity is regulated.
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Affiliation(s)
- Yoav Karpenshif
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States
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Krejci L, Altmannova V, Spirek M, Zhao X. Homologous recombination and its regulation. Nucleic Acids Res 2012; 40:5795-818. [PMID: 22467216 PMCID: PMC3401455 DOI: 10.1093/nar/gks270] [Citation(s) in RCA: 448] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Homologous recombination (HR) is critical both for repairing DNA lesions in mitosis and for chromosomal pairing and exchange during meiosis. However, some forms of HR can also lead to undesirable DNA rearrangements. Multiple regulatory mechanisms have evolved to ensure that HR takes place at the right time, place and manner. Several of these impinge on the control of Rad51 nucleofilaments that play a central role in HR. Some factors promote the formation of these structures while others lead to their disassembly or the use of alternative repair pathways. In this article, we review these mechanisms in both mitotic and meiotic environments and in different eukaryotic taxa, with an emphasis on yeast and mammal systems. Since mutations in several proteins that regulate Rad51 nucleofilaments are associated with cancer and cancer-prone syndromes, we discuss how understanding their functions can lead to the development of better tools for cancer diagnosis and therapy.
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Affiliation(s)
- Lumir Krejci
- Department of Biology, Masaryk University, Brno, Czech Republic.
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31
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Gali H, Juhasz S, Morocz M, Hajdu I, Fatyol K, Szukacsov V, Burkovics P, Haracska L. Role of SUMO modification of human PCNA at stalled replication fork. Nucleic Acids Res 2012; 40:6049-59. [PMID: 22457066 PMCID: PMC3401441 DOI: 10.1093/nar/gks256] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) can be generated not only by reactive agents but also as a result of replication fork collapse at unrepaired DNA lesions. Whereas ubiquitylation of proliferating cell nuclear antigen (PCNA) facilitates damage bypass, modification of yeast PCNA by small ubiquitin-like modifier (SUMO) controls recombination by providing access for the Srs2 helicase to disrupt Rad51 nucleoprotein filaments. However, in human cells, the roles of PCNA SUMOylation have not been explored. Here, we characterize the modification of human PCNA by SUMO in vivo as well as in vitro. We establish that human PCNA can be SUMOylated at multiple sites including its highly conserved K164 residue and that SUMO modification is facilitated by replication factor C (RFC). We also show that expression of SUMOylation site PCNA mutants leads to increased DSB formation in the Rad18−/− cell line where the effect of Rad18-dependent K164 PCNA ubiquitylation can be ruled out. Moreover, expression of PCNA-SUMO1 fusion prevents DSB formation as well as inhibits recombination if replication stalls at DNA lesions. These findings suggest the importance of SUMO modification of human PCNA in preventing replication fork collapse to DSB and providing genome stability.
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Affiliation(s)
- Himabindu Gali
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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32
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Coordinated protein and DNA remodeling by human HLTF on stalled replication fork. Proc Natl Acad Sci U S A 2011; 108:14073-8. [PMID: 21795603 DOI: 10.1073/pnas.1101951108] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Human helicase-like transcription factor (HLTF) exhibits ubiquitin ligase activity for proliferating cell nuclear antigen (PCNA) polyubiquitylation as well as double-stranded DNA translocase activity for remodeling stalled replication fork by fork reversal, which can support damage bypass by template switching. However, a stalled replication fork is surrounded by various DNA-binding proteins which can inhibit the access of damage bypass players, and it is unknown how these proteins become displaced. Here we reveal that HLTF has an ATP hydrolysis-dependent protein remodeling activity, by which it can remove proteins bound to the replication fork. Moreover, we demonstrate that HLTF can displace a broad spectrum of proteins such as replication protein A (RPA), PCNA, and replication factor C (RFC), thereby providing the first example for a protein clearing activity at the stalled replication fork. Our findings clarify how remodeling of a stalled replication fork can occur if it is engaged in interactions with masses of proteins.
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33
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Sebesta M, Burkovics P, Haracska L, Krejci L. Reconstitution of DNA repair synthesis in vitro and the role of polymerase and helicase activities. DNA Repair (Amst) 2011; 10:567-76. [PMID: 21565563 PMCID: PMC3119790 DOI: 10.1016/j.dnarep.2011.03.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 03/04/2011] [Accepted: 03/08/2011] [Indexed: 12/15/2022]
Abstract
The error-free repair of double-strand DNA breaks by homologous recombination (HR) ensures genomic stability using undamaged homologous sequence to copy genetic information. While some of the aspects of the initial steps of HR are understood, the molecular mechanisms underlying events downstream of the D-loop formation remain unclear. Therefore, we have reconstituted D-loop-based in vitro recombination-associated DNA repair synthesis assay and tested the efficacy of polymerases Pol δ and Pol η to extend invaded primer, and the ability of three helicases (Mph1, Srs2 and Sgs1) to displace this extended primer. Both Pol δ and Pol η extended up to 50% of the D-loop substrate, but differed in product length and dependency on proliferating cell nuclear antigen (PCNA). Mph1, but not Srs2 or Sgs1, displaced the extended primer very efficiently, supporting putative role of Mph1 in promoting the synthesis-dependent strand-annealing pathway. The experimental system described here can be employed to increase our understanding of HR events following D-loop formation, as well as the regulatory mechanisms involved.
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Affiliation(s)
- Marek Sebesta
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, Czech Republic
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34
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Abstract
Homologous recombination, the exchange of DNA strands between homologous DNA molecules, is involved in repair of many structural diverse DNA lesions. This versatility stems from multiple ways in which homologous DNA strands can be rearranged. At the core of homologous recombination are recombinase proteins such as RecA and RAD51 that mediate homology recognition and DNA strand exchange through formation of a dynamic nucleoprotein filament. Four stages in the life cycle of nucleoprotein filaments are filament nucleation, filament growth, homologous DNA pairing and strand exchange, and filament dissociation. Progression through this cycle requires a sequence of recombinase-DNA and recombinase protein-protein interactions coupled to ATP binding and hydrolysis. The function of recombinases is controlled by accessory proteins that allow coordination of strand exchange with other steps of homologous recombination and that tailor to the needs of specific aberrant DNA structures undergoing recombination. Accessory proteins are also able to reverse filament formation thereby guarding against inappropriate DNA rearrangements. The dynamic instability of the recombinase-DNA interactions allows both positive and negative action of accessory proteins thereby ensuring that genome maintenance by homologous recombination is not only flexible and versatile, but also accurate.
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35
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Altmannova V, Eckert-Boulet N, Arneric M, Kolesar P, Chaloupkova R, Damborsky J, Sung P, Zhao X, Lisby M, Krejci L. Rad52 SUMOylation affects the efficiency of the DNA repair. Nucleic Acids Res 2010; 38:4708-21. [PMID: 20371517 PMCID: PMC2919706 DOI: 10.1093/nar/gkq195] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Homologous recombination (HR) plays a vital role in DNA metabolic processes including meiosis, DNA repair, DNA replication and rDNA homeostasis. HR defects can lead to pathological outcomes, including genetic diseases and cancer. Recent studies suggest that the post-translational modification by the small ubiquitin-like modifier (SUMO) protein plays an important role in mitotic and meiotic recombination. However, the precise role of SUMOylation during recombination is still unclear. Here, we characterize the effect of SUMOylation on the biochemical properties of the Saccharomyces cerevisiae recombination mediator protein Rad52. Interestingly, Rad52 SUMOylation is enhanced by single-stranded DNA, and we show that SUMOylation of Rad52 also inhibits its DNA binding and annealing activities. The biochemical effects of SUMO modification in vitro are accompanied by a shorter duration of spontaneous Rad52 foci in vivo and a shift in spontaneous mitotic recombination from single-strand annealing to gene conversion events in the SUMO-deficient Rad52 mutants. Taken together, our results highlight the importance of Rad52 SUMOylation as part of a 'quality control' mechanism regulating the efficiency of recombination and DNA repair.
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Affiliation(s)
- Veronika Altmannova
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nadine Eckert-Boulet
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Milica Arneric
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Peter Kolesar
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Radka Chaloupkova
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiri Damborsky
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaolan Zhao
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael Lisby
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA,*To whom correspondence should be addressed. Tel: +420 549493767; Fax: +420 549492556;
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Manthey GM, Bailis AM. Rad51 inhibits translocation formation by non-conservative homologous recombination in Saccharomyces cerevisiae. PLoS One 2010; 5:e11889. [PMID: 20686691 PMCID: PMC2912366 DOI: 10.1371/journal.pone.0011889] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/07/2010] [Indexed: 11/24/2022] Open
Abstract
Chromosomal translocations are a primary biological response to ionizing radiation (IR) exposure, and are likely to result from the inappropriate repair of the DNA double-strand breaks (DSBs) that are created. An abundance of repetitive sequences in eukaryotic genomes provides ample opportunity for such breaks to be repaired by homologous recombination (HR) between non-allelic repeats. Interestingly, in the budding yeast, Saccharomyces cerevisiae the central strand exchange protein, Rad51 that is required for DSB repair by gene conversion between unlinked repeats that conserves genomic structure also suppresses translocation formation by several HR mechanisms. In particular, Rad51 suppresses translocation formation by single-strand annealing (SSA), perhaps the most efficient mechanism for translocation formation by HR in both yeast and mammalian cells. Further, the enhanced translocation formation that emerges in the absence of Rad51 displays a distinct pattern of genetic control, suggesting that this occurs by a separate mechanism. Since hypomorphic mutations in RAD51 in mammalian cells also reduce DSB repair by conservative gene conversion and stimulate non-conservative repair by SSA, this mechanism may also operate in humans and, perhaps contribute to the genome instability that propels the development of cancer.
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Affiliation(s)
- Glenn M. Manthey
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - Adam M. Bailis
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail:
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37
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Schwendener S, Raynard S, Paliwal S, Cheng A, Kanagaraj R, Shevelev I, Stark JM, Sung P, Janscak P. Physical interaction of RECQ5 helicase with RAD51 facilitates its anti-recombinase activity. J Biol Chem 2010; 285:15739-45. [PMID: 20348101 PMCID: PMC2871440 DOI: 10.1074/jbc.m110.110478] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Homologous recombination (HR) provides an efficient mechanism for error-free repair of DNA double-strand breaks (DSBs). However, HR can be also harmful as inappropriate or untimely HR events can give rise to lethal recombination intermediates and chromosome rearrangements. A critical step of HR is the formation of a RAD51 filament on single-stranded (ss)DNA, which mediates the invasion of a homologous DNA molecule. In mammalian cells, several DNA helicases have been implicated in the regulation of this process. RECQ5, a member of the RecQ family of DNA helicases, interacts physically with the RAD51 recombinase and disrupts RAD51 presynaptic filaments in a reaction dependent on ATP hydrolysis. Here, we have precisely mapped the RAD51-interacting domain of RECQ5 and generated mutants that fail to interact with RAD51. We show that although these mutants retain normal ATPase activity, they are impaired in their ability to displace RAD51 from ssDNA. Moreover, we show that ablation of RECQ5-RAD51 complex formation by a point mutation alleviates the inhibitory effect of RECQ5 on HR-mediated DSB repair. These findings provide support for the proposal that interaction with RAD51 is critical for the anti-recombinase attribute of RECQ5.
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Affiliation(s)
- Sybille Schwendener
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
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38
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Abstract
Homologous recombination plays a key role in the maintenance of genome integrity, especially during DNA replication and the repair of double-stranded DNA breaks (DSBs). Just a single un-repaired break can lead to aneuploidy, genetic aberrations or cell death. DSBs are caused by a vast number of both endogenous and exogenous agents including genotoxic chemicals or ionizing radiation, as well as through replication of a damaged template DNA or the replication fork collapse. It is essential for cell survival to recognise and process DSBs as well as other toxic intermediates and launch most appropriate repair mechanism. Many helicases have been implicated to play role in these processes, however their detail roles, specificities and co-operativity in the complex protein-protein interaction networks remain unclear. In this review we summarize the current knowledge about Saccharomyces cerevisiae helicase Srs2 and its effect on multiple DNA metabolic processes that generally affect genome stability. It would appear that Srs2 functions as an “Odd-Job Man” in these processes to make sure that the jobs proceed when and where they are needed.
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Affiliation(s)
- Victoria Marini
- Department of Biology, Faculty of Medicine, Masaryk University, Brno CZ-625 00, Czech Republic
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39
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Shi I, Hallwyl SCL, Seong C, Mortensen U, Rothstein R, Sung P. Role of the Rad52 amino-terminal DNA binding activity in DNA strand capture in homologous recombination. J Biol Chem 2009; 284:33275-84. [PMID: 19812039 DOI: 10.1074/jbc.m109.057752] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Saccharomyces cerevisiae Rad52 protein promotes homologous recombination by nucleating the Rad51 recombinase onto replication protein A-coated single-stranded DNA strands and also by directly annealing such strands. We show that the purified rad52-R70A mutant protein, with a compromised amino-terminal DNA binding domain, is capable of Rad51 delivery to DNA but is deficient in DNA annealing. Results from chromatin immunoprecipitation experiments find that rad52-R70A associates with DNA double-strand breaks and promotes recruitment of Rad51 as efficiently as wild-type Rad52. Analysis of gene conversion intermediates reveals that rad52-R70A cells can mediate DNA strand invasion but are unable to complete the recombination event. These results provide evidence that DNA binding by the evolutionarily conserved amino terminus of Rad52 is needed for the capture of the second DNA end during homologous recombination.
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Affiliation(s)
- Idina Shi
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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