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Mattarocci S. The DNA damage tolerance factor Rad5 and telomere replication. Curr Genet 2025; 71:11. [PMID: 40418329 DOI: 10.1007/s00294-025-01315-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 04/03/2025] [Accepted: 04/22/2025] [Indexed: 05/27/2025]
Abstract
The DNA Damage Tolerance pathway (DDT) is one of the major mechanisms for resolving replication fork blocks. A key factor in DDT is the fork-associated clamp PCNA, which can undergo to mono- or polyubiquitination, leading to error-prone or error-free modes of DNA damage bypass, respectively. In the yeast Saccharomyces cerevisiae, Rad5HLTF/SNF2 factor plays important roles in both pathways: (i) promoting the error-free mode through PCNA polyubiquitination and transient template switching and (ii) interacting with specialized DNA polymerases involved in the error-prone pathway. Rad5 also associates with telomeres, the repetitive DNA regions present at the ends of chromosomes. Telomeric DNA, tightly bound by tandem proteins arrays, poses unique challenges to replication fork progression. Here, I review the current understanding of the link between Rad5 and telomeres and provide evidence that Rad5 binds to yeast telomeres, with notable enrichment during telomere replication. This finding highlights a connection between telomeres and an important DDT factor in unperturbed wild-type cells, raising intriguing possibilities regarding the functional interplay between telomere replication and DNA damage tolerance mechanisms.
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Affiliation(s)
- Stefano Mattarocci
- Université Paris-Saclay, Université Paris-Cité, CEA, Institut de biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, Inserm, France.
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2
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Dvořák Tomaštíková E, Prochazkova K, Yang F, Jemelkova J, Finke A, Dorn A, Said M, Puchta H, Pecinka A. SMC5/6 complex-mediated SUMOylation stimulates DNA-protein cross-link repair in Arabidopsis. THE PLANT CELL 2023; 35:1532-1547. [PMID: 36705512 PMCID: PMC10118267 DOI: 10.1093/plcell/koad020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 05/10/2023]
Abstract
DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis (Arabidopsis thaliana) to date: the endonucleolytic cleavage of DNA by the structure-specific endonuclease MUS81; proteolytic degradation of the crosslinked protein by the metalloprotease WSS1A; and cleavage of the cross-link phosphodiester bonds by the tyrosyl phosphodiesterases TDP1 and TDP2. Here we describe the evolutionary conserved STRUCTURAL MAINTENANCE OF CHROMOSOMEs SMC5/6 complex as a crucial component involved in DPC repair. We identified multiple alleles of the SMC5/6 complex core subunit gene SMC6B via a forward-directed genetic screen designed to identify the factors involved in the repair of DPCs induced by the cytidine analog zebularine. We monitored plant growth and cell death in response to DPC-inducing chemicals, which revealed that the SMC5/6 complex is essential for the repair of several types of DPCs. Genetic interaction and sensitivity assays showed that the SMC5/6 complex works in parallel to the endonucleolytic and proteolytic pathways. The repair of zebularine-induced DPCs was associated with SMC5/6-dependent SUMOylation of the damage sites. Thus, we present the SMC5/6 complex as an important factor in plant DPC repair.
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Affiliation(s)
| | - Klara Prochazkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Fen Yang
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900 Olomouc, Czech Republic
| | - Jitka Jemelkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Functional Genomics and Proteomics, National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | | | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, 12619, Cairo, Egypt
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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Maloisel L, Ma E, Phipps J, Deshayes A, Mattarocci S, Marcand S, Dubrana K, Coïc E. Rad51 filaments assembled in the absence of the complex formed by the Rad51 paralogs Rad55 and Rad57 are outcompeted by translesion DNA polymerases on UV-induced ssDNA gaps. PLoS Genet 2023; 19:e1010639. [PMID: 36749784 PMCID: PMC9937489 DOI: 10.1371/journal.pgen.1010639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 02/17/2023] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
The bypass of DNA lesions that block replicative polymerases during DNA replication relies on DNA damage tolerance pathways. The error-prone translesion synthesis (TLS) pathway depends on specialized DNA polymerases that incorporate nucleotides in front of base lesions, potentially inducing mutagenesis. Two error-free pathways can bypass the lesions: the template switching pathway, which uses the sister chromatid as a template, and the homologous recombination pathway (HR), which also can use the homologous chromosome as template. The balance between error-prone and error-free pathways controls the mutagenesis level. Therefore, it is crucial to precisely characterize factors that influence the pathway choice to better understand genetic stability at replication forks. In yeast, the complex formed by the Rad51 paralogs Rad55 and Rad57 promotes HR and template-switching at stalled replication forks. At DNA double-strand breaks (DSBs), this complex promotes Rad51 filament formation and stability, notably by counteracting the Srs2 anti-recombinase. To explore the role of the Rad55-Rad57 complex in error-free pathways, we monitored the genetic interactions between Rad55-Rad57, the translesion polymerases Polζ or Polη, and Srs2 following UV radiation that induces mostly single-strand DNA gaps. We found that the Rad55-Rad57 complex was involved in three ways. First, it protects Rad51 filaments from Srs2, as it does at DSBs. Second, it promotes Rad51 filament stability independently of Srs2. Finally, we observed that UV-induced HR is almost abolished in Rad55-Rad57 deficient cells, and is partially restored upon Polζ or Polη depletion. Hence, we propose that the Rad55-Rad57 complex is essential to promote Rad51 filament stability on single-strand DNA gaps, notably to counteract the error-prone TLS polymerases and mutagenesis.
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Affiliation(s)
- Laurent Maloisel
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
| | - Emilie Ma
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Jamie Phipps
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Alice Deshayes
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stefano Mattarocci
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Karine Dubrana
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Eric Coïc
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
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4
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Nir Heyman S, Golan M, Liefshitz B, Kupiec M. A Role for the Interactions between Polδ and PCNA Revealed by Analysis of pol3-01 Yeast Mutants. Genes (Basel) 2023; 14:391. [PMID: 36833317 PMCID: PMC9957047 DOI: 10.3390/genes14020391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Several DNA polymerases participate in DNA synthesis during genome replication and DNA repair. PCNA, a homotrimeric ring, acts as a processivity factor for DNA polymerases. PCNA also acts as a "landing pad" for proteins that interact with chromatin and DNA at the moving fork. The interaction between PCNA and polymerase delta (Polδ) is mediated by PIPs (PCNA-interacting peptides), in particular the one on Pol32, a regulatory subunit of Polδ. Here, we demonstrate that pol3-01, an exonuclease mutant of Polδ's catalytic subunit, exhibits a weak interaction with Pol30 compared to the WT DNA polymerase. The weak interaction activates DNA bypass pathways, leading to increased mutagenesis and sister chromatid recombination. Strengthening pol3-01's weak interaction with PCNA suppresses most of the phenotypes. Our results are consistent with a model in which Pol3-01 tends to detach from the chromatin, allowing an easier replacement of Polδ by the trans-lesion synthesis polymerase Zeta (Polz), thus leading to the increased mutagenic phenotype.
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Affiliation(s)
| | | | | | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Ho YC, Ku CS, Tsai SS, Shiu JL, Jiang YZ, Miriam HE, Zhang HW, Chen YT, Chiu WT, Chang SB, Shen CH, Myung K, Chi P, Liaw H. PARP1 recruits DNA translocases to restrain DNA replication and facilitate DNA repair. PLoS Genet 2022; 18:e1010545. [PMID: 36512630 PMCID: PMC9794062 DOI: 10.1371/journal.pgen.1010545] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/27/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
Replication fork reversal which restrains DNA replication progression is an important protective mechanism in response to replication stress. PARP1 is recruited to stalled forks to restrain DNA replication. However, PARP1 has no helicase activity, and the mechanism through which PARP1 participates in DNA replication restraint remains unclear. Here, we found novel protein-protein interactions between PARP1 and DNA translocases, including HLTF, SHPRH, ZRANB3, and SMARCAL1, with HLTF showing the strongest interaction among these DNA translocases. Although HLTF and SHPRH share structural and functional similarity, it remains unclear whether SHPRH contains DNA translocase activity. We further identified the ability of SHPRH to restrain DNA replication upon replication stress, indicating that SHPRH itself could be a DNA translocase or a helper to facilitate DNA translocation. Although hydroxyurea (HU) and MMS induce different types of replication stress, they both induce common DNA replication restraint mechanisms independent of intra-S phase activation. Our results suggest that the PARP1 facilitates DNA translocase recruitment to damaged forks, preventing fork collapse and facilitating DNA repair.
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Affiliation(s)
- Yen-Chih Ho
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Chen-Syun Ku
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Siang-Sheng Tsai
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yi-Zhen Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
| | - Hui Emmanuela Miriam
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Han-Wen Zhang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yen-Tzu Chen
- Department of Public Health & Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Che-Hung Shen
- National Institute of Cancer Research, National Health Research Institutes, Tainan City, Taiwan
| | - Kyungjae Myung
- IBS Center for Genomic Integrity, UNIST-gil 50, Ulsan, Republic of Korea
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei City, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
- * E-mail:
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Kwok ACM, Li C, Lam WT, Wong JTY. Responses of dinoflagellate cells to ultraviolet-C irradiation. Environ Microbiol 2022; 24:5936-5950. [PMID: 35837869 DOI: 10.1111/1462-2920.16135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 01/12/2023]
Abstract
Dinoflagellates are important aquatic microbes and major harmful algal bloom (HAB) agents that form invasive species through ship ballast transfer. UV-C installations are recommended for ballast treatments and HAB controls, but there is a lack of knowledge in dinoflagellate responses to UV-C. We report here dose-dependent cell cycle delay and viability loss of dinoflagellate cells irradiated with UV-C, with significant proliferative reduction at 800 Jm-2 doses or higher, but immediate LD50 was in the range of 2400-3200 Jm-2 . At higher dosages, some dinoflagellate cells surprisingly survived after days of recovery incubation, and continued viability loss, with samples exhibiting DNA fragmentations per proliferative resumption. Sequential cell cycle postponements, suggesting DNA damages were repaired over one cell cycle, were revealed with flow cytometric analysis and transcriptomic analysis. Over a sustained level of other DNA damage repair pathways, transcript elevation was observed only for several components of base pair repair and mismatch repair. Cumulatively, our findings demonstrated special DNA damage responses in dinoflagellate cells, which we discussed in relation to their unique chromo-genomic characters, as well as indicating resilience of dinoflagellate cells to UV-C.
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Affiliation(s)
- Alvin Chun Man Kwok
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Chongping Li
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Wing Tai Lam
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Joseph Tin Yum Wong
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
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Toth R, Halmai M, Gyorfy Z, Balint E, Unk I. The inner side of yeast PCNA contributes to genome stability by mediating interactions with Rad18 and the replicative DNA polymerase δ. Sci Rep 2022; 12:5163. [PMID: 35338218 PMCID: PMC8956578 DOI: 10.1038/s41598-022-09208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/14/2022] [Indexed: 11/09/2022] Open
Abstract
PCNA is a central orchestrator of cellular processes linked to DNA metabolism. It is a binding platform for a plethora of proteins and coordinates and regulates the activity of several pathways. The outer side of PCNA comprises most of the known interacting and regulatory surfaces, whereas the residues at the inner side constitute the sliding surface facing the DNA double helix. Here, by investigating the L154A mutation found at the inner side, we show that the inner surface mediates protein interactions essential for genome stability. It forms part of the binding site of Rad18, a key regulator of DNA damage tolerance, and is required for PCNA sumoylation which prevents unscheduled recombination during replication. In addition, the L154 residue is necessary for stable complex formation between PCNA and the replicative DNA polymerase δ. Hence, its absence increases the mutation burden of yeast cells due to faulty replication. In summary, the essential role of the L154 of PCNA in guarding and maintaining stable replication and promoting DNA damage tolerance reveals a new connection between these processes and assigns a new coordinating function to the central channel of PCNA.
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Affiliation(s)
- Robert Toth
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Miklos Halmai
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Zsuzsanna Gyorfy
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Eva Balint
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Ildiko Unk
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary.
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Manohar K, Khandagale P, Patel SK, Sahu JK, Acharya N. The ubiquitin-binding domain of DNA polymerase η directly binds to DNA clamp PCNA and regulates translesion DNA synthesis. J Biol Chem 2022; 298:101506. [PMID: 34929163 PMCID: PMC8784325 DOI: 10.1016/j.jbc.2021.101506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/01/2022] Open
Abstract
DNA polymerase eta (Polη) is a unique translesion DNA synthesis (TLS) enzyme required for the error-free bypass of ultraviolet ray (UV)-induced cyclobutane pyrimidine dimers in DNA. Therefore, its deficiency confers cellular sensitivity to UV radiation and an increased rate of UV-induced mutagenesis. Polη possesses a ubiquitin-binding zinc finger (ubz) domain and a PCNA-interacting-protein (pip) motif in the carboxy-terminal region. The role of the Polη pip motif in PCNA interaction required for DNA polymerase recruitment to the stalled replication fork has been demonstrated in earlier studies; however, the function of the ubz domain remains divisive. As per the current notion, the ubz domain of Polη binds to the ubiquitin moiety of the ubiquitinated PCNA, but such interaction is found to be nonessential for Polη's function. In this study, through amino acid sequence alignments, we identify three classes of Polη among different species based on the presence or absence of pip motif or ubz domain and using comprehensive mutational analyses, we show that the ubz domain of Polη, which intrinsically lacks the pip motif directly binds to the interdomain connecting loop (IDCL) of PCNA and regulates Polη's TLS activity. We further propose two distinct modes of PCNA interaction mediated either by pip motif or ubz domain in various Polη homologs. When the pip motif or ubz domain of a given Polη binds to the IDCL of PCNA, such interaction becomes essential, whereas the binding of ubz domain to PCNA through ubiquitin is dispensable for Polη's function.
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Affiliation(s)
- Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India; Regional Centre for Biotechnology, Faridabad, India
| | - Jugal Kishor Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India; Regional Centre for Biotechnology, Faridabad, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.
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Toth R, Balogh D, Pinter L, Jaksa G, Szeplaki B, Graf A, Gyorfy Z, Enyedi MZ, Kiss E, Haracska L, Unk I. The Rad5 Helicase and RING Domains Contribute to Genome Stability through their Independent Catalytic Activities. J Mol Biol 2022; 434:167437. [PMID: 34990655 DOI: 10.1016/j.jmb.2021.167437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/08/2021] [Accepted: 12/28/2021] [Indexed: 11/27/2022]
Abstract
Genomic stability is compromised by DNA damage that obstructs replication. Rad5 plays a prominent role in DNA damage bypass processes that evolved to ensure the continuation of stalled replication. Like its human orthologs, the HLTF and SHPRH tumor suppressors, yeast Rad5 has a RING domain that supports ubiquitin ligase activity promoting PCNA polyubiquitylation and a helicase domain that in the case of HLTF and Rad5 was shown to exhibit an ATPase-linked replication fork reversal activity. The RING domain is embedded in the helicase domain, confusing their separate investigation and the understanding of the exact role of Rad5 in DNA damage bypass. Particularly, it is still debated whether the helicase domain plays a catalytic or a non-enzymatic role during error-free damage bypass and whether it facilitates a function separately from the RING domain. In this study, through in vivo and in vitro characterization of domain-specific mutants, we delineate the contributions of the two domains to Rad5 function. Yeast genetic experiments and whole-genome sequencing complemented with biochemical assays demonstrate that the ubiquitin ligase and the ATPase-linked activities of Rad5 exhibit independent catalytic activities in facilitating separate pathways during error-free lesion bypass. Our results also provide important insights into the mutagenic role of Rad5 and indicate its tripartite contribution to DNA damage tolerance.
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Affiliation(s)
- Robert Toth
- DNA Repair Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary; University of Szeged, Doctoral School of Biology, Hungary
| | - David Balogh
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | | | | | | | - Alexandra Graf
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Zsuzsanna Gyorfy
- DNA Repair Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Marton Zs Enyedi
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary; Delta Bio 2000 Ltd., Szeged H-6726, Hungary
| | - Erno Kiss
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Ildiko Unk
- DNA Repair Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary.
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Thivolle A, Mehnert AK, Tihon E, McLaughlin E, Dujeancourt-Henry A, Glover L. DNA double strand break position leads to distinct gene expression changes and regulates VSG switching pathway choice. PLoS Pathog 2021; 17:e1010038. [PMID: 34767618 PMCID: PMC8612549 DOI: 10.1371/journal.ppat.1010038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/24/2021] [Accepted: 10/14/2021] [Indexed: 12/11/2022] Open
Abstract
Antigenic variation is an immune evasion strategy used by Trypanosoma brucei that results in the periodic exchange of the surface protein coat. This process is facilitated by the movement of variant surface glycoprotein genes in or out of a specialized locus known as bloodstream form expression site by homologous recombination, facilitated by blocks of repetitive sequence known as the 70-bp repeats, that provide homology for gene conversion events. DNA double strand breaks are potent drivers of antigenic variation, however where these breaks must fall to elicit a switch is not well understood. To understand how the position of a break influences antigenic variation we established a series of cell lines to study the effect of an I-SceI meganuclease break in the active expression site. We found that a DNA break within repetitive regions is not productive for VSG switching, and show that the break position leads to a distinct gene expression profile and DNA repair response which dictates how antigenic variation proceeds in African trypanosomes. Crucial to triggering antigenic variation is the formation of DNA double strand breaks (DSB). These lesions have been shown to be potent drivers of variant surface glycoprotein (VSG) switching, albeit highly toxic. Trypanosomes immune evasion strategy relies on their ability to rapidly exchange the singly expressed VSG for one that is antigenically distinct. It has been previously shown that the subtelomeric ends, here the locus from which the VSG is expressed, accumulate DSBs. Using the I-SceI meganuclease system we established a series of cell lines to assess how the position of a DSB influences antigenic variation and the cellular response to a break. We show that a DSB in highly repetitive regions are poor triggers for antigenic variation. Contrastingly, a DSB that does lead to VSG switching via recombination results in the upregulation of DNA damage linked genes. Our results provide new insights into how the position of a DSB influences repair pathway choice and the subsequent gene expression changes. We propose that where repair is not dominated by recombination, but rather by an error prone mechanism, silent BES promoters are partially activated to facilitate rapid transcriptional switching should repair be deleterious to the cell.
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Affiliation(s)
- Alix Thivolle
- Institut Pasteur, Université de Paris, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Ann-Kathrin Mehnert
- Institut Pasteur, Université de Paris, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Eliane Tihon
- Institut Pasteur, Université de Paris, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Emilia McLaughlin
- Institut Pasteur, Université de Paris, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Annick Dujeancourt-Henry
- Institut Pasteur, Université de Paris, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Lucy Glover
- Institut Pasteur, Université de Paris, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
- * E-mail:
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11
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Arbel M, Liefshitz B, Kupiec M. DNA damage bypass pathways and their effect on mutagenesis in yeast. FEMS Microbiol Rev 2021; 45:5896953. [PMID: 32840566 DOI: 10.1093/femsre/fuaa038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
What is the origin of mutations? In contrast to the naïve notion that mutations are unfortunate accidents, genetic research in microorganisms has demonstrated that most mutations are created by genetically encoded error-prone repair mechanisms. However, error-free repair pathways also exist, and it is still unclear how cells decide when to use one repair method or the other. Here, we summarize what is known about the DNA damage tolerance mechanisms (also known as post-replication repair) for perhaps the best-studied organism, the yeast Saccharomyces cerevisiae. We describe the latest research, which has established the existence of at least two error-free and two error-prone inter-related mechanisms of damage tolerance that compete for the handling of spontaneous DNA damage. We explore what is known about the induction of mutations by DNA damage. We point to potential paradoxes and to open questions that still remain unanswered.
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Affiliation(s)
- Matan Arbel
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Batia Liefshitz
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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12
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Wong RP, Petriukov K, Ulrich HD. Daughter-strand gaps in DNA replication - substrates of lesion processing and initiators of distress signalling. DNA Repair (Amst) 2021; 105:103163. [PMID: 34186497 DOI: 10.1016/j.dnarep.2021.103163] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
Dealing with DNA lesions during genome replication is particularly challenging because damaged replication templates interfere with the progression of the replicative DNA polymerases and thereby endanger the stability of the replisome. A variety of mechanisms for the recovery of replication forks exist, but both bacteria and eukaryotic cells also have the option of continuing replication downstream of the lesion, leaving behind a daughter-strand gap in the newly synthesized DNA. In this review, we address the significance of these single-stranded DNA structures as sites of DNA damage sensing and processing at a distance from ongoing genome replication. We describe the factors controlling the emergence of daughter-strand gaps from stalled replication intermediates, the benefits and risks of their expansion and repair via translesion synthesis or recombination-mediated template switching, and the mechanisms by which they activate local as well as global replication stress signals. Our growing understanding of daughter-strand gaps not only identifies them as targets of fundamental genome maintenance mechanisms, but also suggests that proper control over their activities has important practical implications for treatment strategies and resistance mechanisms in cancer therapy.
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Affiliation(s)
- Ronald P Wong
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany
| | - Kirill Petriukov
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany.
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13
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Frittmann O, Gali VK, Halmai M, Toth R, Gyorfy Z, Balint E, Unk I. The Zn-finger of Saccharomyces cerevisiae Rad18 and its adjacent region mediate interaction with Rad5. G3-GENES GENOMES GENETICS 2021; 11:6133228. [PMID: 33570581 PMCID: PMC8759821 DOI: 10.1093/g3journal/jkab041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 11/13/2022]
Abstract
DNA damages that hinder the movement of the replication complex can ultimately lead to cell death. To avoid that, cells possess several DNA damage bypass mechanisms. The Rad18 ubiquitin ligase controls error-free and mutagenic pathways that help the replication complex to bypass DNA lesions by monoubiquitylating PCNA at stalled replication forks. In Saccharomyces cerevisiae, two of the Rad18 governed pathways are activated by monoubiquitylated PCNA and they involve translesion synthesis polymerases, whereas a third pathway needs subsequent polyubiquitylation of the same PCNA residue by another ubiquitin ligase the Rad5 protein, and it employs template switching. The goal of this study was to dissect the regulatory role of the multidomain Rad18 in DNA damage bypass using a structure-function based approach. Investigating deletion and point mutant RAD18 variants in yeast genetic and yeast two-hybrid assays we show that the Zn-finger of Rad18 mediates its interaction with Rad5, and the N-terminal adjacent region is also necessary for Rad5 binding. Moreover, results of the yeast two-hybrid and in vivo ubiquitylation experiments raise the possibility that direct interaction between Rad18 and Rad5 might not be necessary for the function of the Rad5 dependent pathway. The presented data also reveal that yeast Rad18 uses different domains to mediate its association with itself and with Rad5. Our results contribute to better understanding of the complex machinery of DNA damage bypass pathways.
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Affiliation(s)
- Orsolya Frittmann
- Biological Research Centre, Szeged, Eotvos Loránd Research Network, The Institute of Genetics, Szeged, H-6726, Hungary.,Doctoral School of Biology, University of Szeged, Szeged, H-6720, Hungary
| | - Vamsi K Gali
- Biological Research Centre, Szeged, Eotvos Loránd Research Network, The Institute of Genetics, Szeged, H-6726, Hungary
| | - Miklos Halmai
- Biological Research Centre, Szeged, Eotvos Loránd Research Network, The Institute of Genetics, Szeged, H-6726, Hungary
| | - Robert Toth
- Biological Research Centre, Szeged, Eotvos Loránd Research Network, The Institute of Genetics, Szeged, H-6726, Hungary
| | - Zsuzsanna Gyorfy
- Biological Research Centre, Szeged, Eotvos Loránd Research Network, The Institute of Genetics, Szeged, H-6726, Hungary
| | - Eva Balint
- Biological Research Centre, Szeged, Eotvos Loránd Research Network, The Institute of Genetics, Szeged, H-6726, Hungary
| | - Ildiko Unk
- Biological Research Centre, Szeged, Eotvos Loránd Research Network, The Institute of Genetics, Szeged, H-6726, Hungary
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14
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Alekseeva EA, Korolev VG. DNA Damage Tolerance in the Yeast Saccharomyces cerevisiae. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421040025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Du X, Song H, Shen N, Hua R, Yang G. The Molecular Basis of Ubiquitin-Conjugating Enzymes (E2s) as a Potential Target for Cancer Therapy. Int J Mol Sci 2021; 22:ijms22073440. [PMID: 33810518 PMCID: PMC8037234 DOI: 10.3390/ijms22073440] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 01/06/2023] Open
Abstract
Ubiquitin-conjugating enzymes (E2s) are one of the three enzymes required by the ubiquitin-proteasome pathway to connect activated ubiquitin to target proteins via ubiquitin ligases. E2s determine the connection type of the ubiquitin chains, and different types of ubiquitin chains regulate the stability and activity of substrate proteins. Thus, E2s participate in the regulation of a variety of biological processes. In recent years, the importance of E2s in human health and diseases has been particularly emphasized. Studies have shown that E2s are dysregulated in variety of cancers, thus it might be a potential therapeutic target. However, the molecular basis of E2s as a therapeutic target has not been described systematically. We reviewed this issue from the perspective of the special position and role of E2s in the ubiquitin-proteasome pathway, the structure of E2s and biological processes they are involved in. In addition, the inhibitors and microRNAs targeting E2s are also summarized. This article not only provides a direction for the development of effective drugs but also lays a foundation for further study on this enzyme in the future.
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16
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Halas A, Fijak-Moskal J, Kuberska R, Murcia Pienkowski V, Kaniak-Golik A, Pollak A, Poznanski J, Rydzanicz M, Bik-Multanowski M, Sledziewska-Gojska E, Płoski R. Developmental delay with hypotrophy associated with homozygous functionally relevant REV3L variant. J Mol Med (Berl) 2021; 99:415-423. [PMID: 33474647 DOI: 10.1007/s00109-020-02033-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/07/2020] [Accepted: 12/23/2020] [Indexed: 11/29/2022]
Abstract
REV3L encodes a catalytic subunit of DNA polymerase zeta (Pol zeta) which is essential for the tolerance of DNA damage by inducing translesion synthesis (TLS). So far, the only Mendelian disease associated with REV3L was Moebius syndrome (3 patients with dominant REV3L mutations causing monoallelic loss-of-function were reported). We describe a homozygous ultra-rare REV3L variant (T2753R) identified with whole exome sequencing in a child without Moebius syndrome but with developmental delay, hypotrophy, and dysmorphic features who was born to healthy parents (heterozygous carriers of the variant). The variant affects the amino acid adjacent to functionally important KKRY motif. By introducing an equivalent mutation (S1192R) into the REV3 gene in yeasts, we showed that, whereas it retained residual function, it caused clear dysfunction of TLS in the nucleus and instability of mitochondrial genetic information. In particular, the mutation increased UV sensitivity measured by cell survival, decreased both the spontaneous (P < 0.005) and UV-induced (P < 0.0001) mutagenesis rates of nuclear DNA and increased the UV-induced mutagenesis rates of mitochondrial DNA (P < 0.0005). We propose that our proband is the first reported case of a REV3L associated disease different from Moebius syndrome both in terms of clinical manifestations and inheritance (autosomal recessive rather than dominant). KEY MESSAGES: First description of a human recessive disorder associated with a REV3L variant. A study in yeast showed that the variant affected the enzymatic function of the protein. In particular, it caused increased UV sensitivity and abnormal mutagenesis rates.
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Affiliation(s)
- Agnieszka Halas
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Jolanta Fijak-Moskal
- Department of Medical Genetics, Jagiellonian University Medical College, 30-663, Krakow, Poland
| | - Renata Kuberska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, 02-106, Warsaw, Poland.,Ardigen, Podole 76, 30-394, Krakow, Poland
| | - Aneta Kaniak-Golik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, 02-106, Warsaw, Poland
| | - Jarosław Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Malgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106, Warsaw, Poland
| | | | - Ewa Sledziewska-Gojska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland.
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106, Warsaw, Poland.
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17
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Cano‐Linares MI, Yáñez‐Vilches A, García‐Rodríguez N, Barrientos‐Moreno M, González‐Prieto R, San‐Segundo P, Ulrich HD, Prado F. Non-recombinogenic roles for Rad52 in translesion synthesis during DNA damage tolerance. EMBO Rep 2021; 22:e50410. [PMID: 33289333 PMCID: PMC7788459 DOI: 10.15252/embr.202050410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 01/09/2023] Open
Abstract
DNA damage tolerance relies on homologous recombination (HR) and translesion synthesis (TLS) mechanisms to fill in the ssDNA gaps generated during passing of the replication fork over DNA lesions in the template. Whereas TLS requires specialized polymerases able to incorporate a dNTP opposite the lesion and is error-prone, HR uses the sister chromatid and is mostly error-free. We report that the HR protein Rad52-but not Rad51 and Rad57-acts in concert with the TLS machinery (Rad6/Rad18-mediated PCNA ubiquitylation and polymerases Rev1/Pol ζ) to repair MMS and UV light-induced ssDNA gaps through a non-recombinogenic mechanism, as inferred from the different phenotypes displayed in the absence of Rad52 and Rad54 (essential for MMS- and UV-induced HR); accordingly, Rad52 is required for efficient DNA damage-induced mutagenesis. In addition, Rad52, Rad51, and Rad57, but not Rad54, facilitate Rad6/Rad18 binding to chromatin and subsequent DNA damage-induced PCNA ubiquitylation. Therefore, Rad52 facilitates the tolerance process not only by HR but also by TLS through Rad51/Rad57-dependent and -independent processes, providing a novel role for the recombination proteins in maintaining genome integrity.
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Affiliation(s)
- María I Cano‐Linares
- Department of Genome BiologyAndalusian Molecular Biology and Regenerative Medicine Center (CABIMER)CSIC‐University of Seville‐University Pablo de OlavideSevilleSpain
| | - Aurora Yáñez‐Vilches
- Department of Genome BiologyAndalusian Molecular Biology and Regenerative Medicine Center (CABIMER)CSIC‐University of Seville‐University Pablo de OlavideSevilleSpain
| | - Néstor García‐Rodríguez
- Institute of Molecular Biology (IMB)MainzGermany
- Present address:
Department of Genome BiologyAndalusian Molecular Biology and Regenerative Medicine Center (CABIMER)CSIC‐University of Seville‐University Pablo de OlavideSevilleSpain
| | - Marta Barrientos‐Moreno
- Department of Genome BiologyAndalusian Molecular Biology and Regenerative Medicine Center (CABIMER)CSIC‐University of Seville‐University Pablo de OlavideSevilleSpain
| | - Román González‐Prieto
- Department of Genome BiologyAndalusian Molecular Biology and Regenerative Medicine Center (CABIMER)CSIC‐University of Seville‐University Pablo de OlavideSevilleSpain
- Present address:
Department of Cell and Chemical BiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Pedro San‐Segundo
- Institute of Functional Biology and Genomics (IBFG)CSIC‐University of SalamancaSalamancaSpain
| | | | - Félix Prado
- Department of Genome BiologyAndalusian Molecular Biology and Regenerative Medicine Center (CABIMER)CSIC‐University of Seville‐University Pablo de OlavideSevilleSpain
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18
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Conti BA, Smogorzewska A. Mechanisms of direct replication restart at stressed replisomes. DNA Repair (Amst) 2020; 95:102947. [PMID: 32853827 PMCID: PMC7669714 DOI: 10.1016/j.dnarep.2020.102947] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/09/2023]
Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA.
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19
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Dhakal S, Macreadie I. Protein Homeostasis Networks and the Use of Yeast to Guide Interventions in Alzheimer's Disease. Int J Mol Sci 2020; 21:E8014. [PMID: 33126501 PMCID: PMC7662794 DOI: 10.3390/ijms21218014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's Disease (AD) is a progressive multifactorial age-related neurodegenerative disorder that causes the majority of deaths due to dementia in the elderly. Although various risk factors have been found to be associated with AD progression, the cause of the disease is still unresolved. The loss of proteostasis is one of the major causes of AD: it is evident by aggregation of misfolded proteins, lipid homeostasis disruption, accumulation of autophagic vesicles, and oxidative damage during the disease progression. Different models have been developed to study AD, one of which is a yeast model. Yeasts are simple unicellular eukaryotic cells that have provided great insights into human cell biology. Various yeast models, including unmodified and genetically modified yeasts, have been established for studying AD and have provided significant amount of information on AD pathology and potential interventions. The conservation of various human biological processes, including signal transduction, energy metabolism, protein homeostasis, stress responses, oxidative phosphorylation, vesicle trafficking, apoptosis, endocytosis, and ageing, renders yeast a fascinating, powerful model for AD. In addition, the easy manipulation of the yeast genome and availability of methods to evaluate yeast cells rapidly in high throughput technological platforms strengthen the rationale of using yeast as a model. This review focuses on the description of the proteostasis network in yeast and its comparison with the human proteostasis network. It further elaborates on the AD-associated proteostasis failure and applications of the yeast proteostasis network to understand AD pathology and its potential to guide interventions against AD.
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Affiliation(s)
| | - Ian Macreadie
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia;
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20
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Contractions of the C-Terminal Domain of Saccharomyces cerevisiae Rpb1p Are Mediated by Rad5p. G3-GENES GENOMES GENETICS 2020; 10:2543-2551. [PMID: 32467128 PMCID: PMC7341143 DOI: 10.1534/g3.120.401409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The C-terminal domain (CTD) is an essential domain of the largest subunit of RNA polymerase II, Rpb1p, and is composed of 26 tandem repeats of a seven-amino acid sequence, YSPTSPS. Despite being an essential domain within an essential gene, we have previously demonstrated that the CTD coding region is genetically unstable. Furthermore, yeast with a truncated or mutated CTD sequence are capable of promoting spontaneous genetic expansion or contraction of this coding region to improve fitness. We investigated the mechanism by which the CTD contracts using a tet-off reporter system for RPB1 to monitor genetic instability within the CTD coding region. We report that contractions require the post-replication repair factor Rad5p but, unlike expansions, not the homologous recombination factors Rad51p and Rad52p. Sequence analysis of contraction events reveals that deleted regions are flanked by microhomologies. We also find that G-quadruplex forming sequences predicted by the QGRS Mapper are enriched on the noncoding strand of the CTD compared to the body of RPB1. Formation of G-quadruplexes in the CTD coding region could block the replication fork, necessitating post-replication repair. We propose that contractions of the CTD result when microhomologies misalign during Rad5p-dependent template switching via fork reversal.
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21
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MutSα deficiency increases tolerance to DNA damage in yeast lacking postreplication repair. DNA Repair (Amst) 2020; 91-92:102870. [PMID: 32470850 DOI: 10.1016/j.dnarep.2020.102870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/16/2020] [Accepted: 04/26/2020] [Indexed: 11/22/2022]
Abstract
By combining mutations in DNA repair genes, important and unexpected interactions between different repair pathways can be discovered. In this study, we identified a novel link between mismatch repair (MMR) genes and postreplication repair (PRR) in Saccharomyces cerevisiae. Strains lacking Rad5 (HLTF in mammals), a protein important for restarting stalled replication forks in the error-free PRR pathway, were supersensitive to the DNA methylating agent methyl methanesulfonate (MMS). Deletion of the mismatch repair genes, MSH2 or MSH6, which together constitutes the MutSα complex, partially suppressed the MMS super-sensitivity of the rad5Δ strain. Deletion of MSH2 also suppressed the MMS sensitivity of mms2Δ, which acts together with Rad5 in error-free PRR. However, inactivating the mismatch repair genes MSH3 and MLH1 did not suppress rad5Δ, showing that the suppression was specific for disabling MutSα. The partial suppression did not require translesion DNA synthesis (REV1, REV3 or RAD30), base excision repair (MAG1) or homologous recombination (RAD51). Instead, the underlying mechanism was dependent on RAD52 while independent of established pathways involving RAD52, like single-strand annealing and break-induced replication. We propose a Rad5- and Rad51-independent template switch pathway, capable of compensating for the loss of the error-free template-switch subpathway of postreplication repair, triggered by the loss of MutSα.
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22
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Masuda Y, Masutani C. Spatiotemporal regulation of PCNA ubiquitination in damage tolerance pathways. Crit Rev Biochem Mol Biol 2019; 54:418-442. [PMID: 31736364 DOI: 10.1080/10409238.2019.1687420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA is constantly exposed to a wide variety of exogenous and endogenous agents, and most DNA lesions inhibit DNA synthesis. To cope with such problems during replication, cells have molecular mechanisms to resume DNA synthesis in the presence of DNA lesions, which are known as DNA damage tolerance (DDT) pathways. The concept of ubiquitination-mediated regulation of DDT pathways in eukaryotes was established via genetic studies in the yeast Saccharomyces cerevisiae, in which two branches of the DDT pathway are regulated via ubiquitination of proliferating cell nuclear antigen (PCNA): translesion DNA synthesis (TLS) and homology-dependent repair (HDR), which are stimulated by mono- and polyubiquitination of PCNA, respectively. Over the subsequent nearly two decades, significant progress has been made in understanding the mechanisms that regulate DDT pathways in other eukaryotes. Importantly, TLS is intrinsically error-prone because of the miscoding nature of most damaged nucleotides and inaccurate replication of undamaged templates by TLS polymerases (pols), whereas HDR is theoretically error-free because the DNA synthesis is thought to be predominantly performed by pol δ, an accurate replicative DNA pol, using the undamaged sister chromatid as its template. Thus, the regulation of the choice between the TLS and HDR pathways is critical to determine the appropriate biological outcomes caused by DNA damage. In this review, we summarize our current understanding of the species-specific regulatory mechanisms of PCNA ubiquitination and how cells choose between TLS and HDR. We then provide a hypothetical model for the spatiotemporal regulation of DDT pathways in human cells.
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Affiliation(s)
- Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
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23
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Abe T, Branzei D, Hirota K. DNA Damage Tolerance Mechanisms Revealed from the Analysis of Immunoglobulin V Gene Diversification in Avian DT40 Cells. Genes (Basel) 2018; 9:genes9120614. [PMID: 30544644 PMCID: PMC6316486 DOI: 10.3390/genes9120614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 01/19/2023] Open
Abstract
DNA replication is an essential biochemical reaction in dividing cells that frequently stalls at damaged sites. Homologous/homeologous recombination (HR)-mediated template switch and translesion DNA synthesis (TLS)-mediated bypass processes release arrested DNA replication forks. These mechanisms are pivotal for replication fork maintenance and play critical roles in DNA damage tolerance (DDT) and gap-filling. The avian DT40 B lymphocyte cell line provides an opportunity to examine HR-mediated template switch and TLS triggered by abasic sites by sequencing the constitutively diversifying immunoglobulin light-chain variable gene (IgV). During IgV diversification, activation-induced deaminase (AID) converts dC to dU, which in turn is excised by uracil DNA glycosylase and yields abasic sites within a defined window of around 500 base pairs. These abasic sites can induce gene conversion with a set of homeologous upstream pseudogenes via the HR-mediated template switch, resulting in templated mutagenesis, or can be bypassed directly by TLS, resulting in non-templated somatic hypermutation at dC/dG base pairs. In this review, we discuss recent works unveiling IgV diversification mechanisms in avian DT40 cells, which shed light on DDT mode usage in vertebrate cells and tolerance of abasic sites.
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Affiliation(s)
- Takuya Abe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
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24
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Abstract
Mutations are the root source of genetic variation and underlie the process of evolution. Although the rates at which mutations occur vary considerably between species, little is known about differences within species, or the genetic and molecular basis of these differences. Here, we leveraged the power of the yeast Saccharomyces cerevisiae as a model system to uncover natural genetic variants that underlie variation in mutation rate. We developed a high-throughput fluctuation assay and used it to quantify mutation rates in seven natural yeast isolates and in 1040 segregant progeny from a cross between BY, a laboratory strain, and RM, a wine strain. We observed that mutation rate varies among yeast strains and is heritable (H2 = 0.49). We performed linkage mapping in the segregants and identified four quantitative trait loci underlying mutation rate variation in the cross. We fine-mapped two quantitative trait loci to the underlying causal genes, RAD5 and MKT1, that contribute to mutation rate variation. These genes also underlie sensitivity to the DNA-damaging agents 4NQO and MMS, suggesting a connection between spontaneous mutation rate and mutagen sensitivity.
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25
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SUMOylation of PCNA by PIAS1 and PIAS4 promotes template switch in the chicken and human B cell lines. Proc Natl Acad Sci U S A 2018; 115:12793-12798. [PMID: 30487218 DOI: 10.1073/pnas.1716349115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA damage tolerance (DDT) releases replication blockage caused by damaged nucleotides on template strands employing two alternative pathways, error-prone translesion DNA synthesis (TLS) and error-free template switch (TS). Lys164 of proliferating cell nuclear antigen (PCNA) is SUMOylated during the physiological cell cycle. To explore the role for SUMOylation of PCNA in DDT, we characterized chicken DT40 and human TK6 B cells deficient in the PIAS1 and PIAS4 small ubiquitin-like modifier (SUMO) E3 ligases. DT40 cells have a unique advantage in the phenotypic analysis of DDT as they continuously diversify their immunoglobulin (Ig) variable genes by TLS and TS [Ig gene conversion (GC)], both relieving replication blocks at abasic sites without accompanying by DNA breakage. Remarkably, PIAS1 -/- /PIAS4 -/- cells displayed a multifold decrease in SUMOylation of PCNA at Lys164 and over a 90% decrease in the rate of TS. Likewise, PIAS1 -/- /PIAS4 -/- TK6 cells showed a shift of DDT from TS to TLS at a chemosynthetic UV lesion inserted into the genomic DNA. The PCNA K164R/K164R mutation caused a ∼90% decrease in the rate of Ig GC and no additional impact on PIAS1 -/- /PIAS4 -/- cells. This epistatic relationship between the PCNA K164R/K164R and the PIAS1 -/- /PIAS4 -/- mutations suggests that PIAS1 and PIAS4 promote TS mainly through SUMOylation of PCNA at Lys164. This idea is further supported by the data that overexpression of a PCNA-SUMO1 chimeric protein restores defects in TS in PIAS1 -/- /PIAS4 -/- cells. In conclusion, SUMOylation of PCNA at Lys164 promoted by PIAS1 and PIAS4 ensures the error-free release of replication blockage during physiological DNA replication in metazoan cells.
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26
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Sutherland JH, Holloman WK. Loss of Cohesin Subunit Rec8 Switches Rad51 Mediator Dependence in Resistance to Formaldehyde Toxicity in Ustilago maydis. Genetics 2018; 210:559-572. [PMID: 30082279 PMCID: PMC6216591 DOI: 10.1534/genetics.118.301439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/03/2018] [Indexed: 01/08/2023] Open
Abstract
DNA-protein cross-links (DPCs) are frequently occurring lesions that provoke continual threats to the integrity of the genome by interference with replication and transcription. Reactive aldehydes generated from endogenous metabolic processes or produced in the environment are sources that trigger cross-linking of DNA with associated proteins. DNA repair pathways in place for removing DPCs, or for bypassing them to enable completion of replication, include homologous recombination (HR) and replication fork remodeling (FR) systems. Here, we surveyed a set of mutants defective in known HR and FR components to determine their contribution toward maintaining resistance to chronic formaldehyde (FA) exposure in Ustilago maydis, a fungus that relies on the BRCA2-family member Brh2 as the principal Rad51 mediator in repair of DNA strand breaks. We found that, in addition to Brh2, Rad52 was also vital for resistance to FA. Deleting the gene for Rec8, a kleisin subunit of cohesin, eliminated the requirement for Brh2, but not Rad52, in FA resistance. The Rad51K133R mutant variant that is able to bind DNA but unable to dissociate from it was able to support resistance to FA. These findings suggest a model for DPC repair and tolerance that features a specialized role for Rad52, enabling Rad51 to access DNA in its noncanonical capacity of replication fork protection rather than DNA strand transfer.
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Affiliation(s)
- Jeanette H Sutherland
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
| | - William K Holloman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
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Nakazato A, Kajita K, Ooka M, Akagawa R, Abe T, Takeda S, Branzei D, Hirota K. SPARTAN promotes genetic diversification of the immunoglobulin-variable gene locus in avian DT40 cells. DNA Repair (Amst) 2018; 68:50-57. [PMID: 29935364 DOI: 10.1016/j.dnarep.2018.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 11/17/2022]
Abstract
Prolonged replication arrest on damaged templates is a cause of fork collapse, potentially resulting in genome instability. Arrested replication is rescued by translesion DNA synthesis (TLS) and homologous recombination (HR)-mediated template switching. SPARTAN, a ubiquitin-PCNA-interacting regulator, regulates TLS via mechanisms incompletely understood. Here we show that SPARTAN promotes diversification of the chicken DT40 immunoglobulin-variable λ gene by facilitating TLS-mediated hypermutation and template switch-mediated gene-conversion, both induced by replication blocks at abasic sites. SPARTAN-/- and SPARTAN-/-/Polη-/-/Polζ-/- cells showed defective and similar decrease in hypermutation rates, as well as alterations in the mutation spectra, with decreased dG-to-dC transversions and increased dG-to-dA transitions. Strikingly, SPARTAN-/- cells also showed reduced template switch-mediated gene-conversion at the immunoglobulin locus, while being proficient in HR-mediated double strand break repair, and sister chromatid recombination. Notably, SPARTAN's ubiquitin-binding zinc-finger 4 domain, but not the PCNA interacting peptide domain or its DNA-binding domain, was specifically required for the promotion of immunoglobulin gene-conversion, while all these three domains were shown to contribute similarly to TLS. In all, our results suggest that SPARTAN mediates TLS in concert with the Polη-Polζ pathway and that it facilitates HR-mediated template switching at a subset of stalled replication forks, potentially by interacting with unknown ubiquitinated proteins.
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Affiliation(s)
- Arisa Nakazato
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Kinumi Kajita
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Masato Ooka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Remi Akagawa
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Takuya Abe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan; IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Dana Branzei
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy.
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan.
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The translesion DNA polymerases Pol ζ and Rev1 are activated independently of PCNA ubiquitination upon UV radiation in mutants of DNA polymerase δ. PLoS Genet 2017; 13:e1007119. [PMID: 29281621 PMCID: PMC5760103 DOI: 10.1371/journal.pgen.1007119] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/09/2018] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Replicative DNA polymerases cannot insert efficiently nucleotides at sites of base lesions. This function is taken over by specialized translesion DNA synthesis (TLS) polymerases to allow DNA replication completion in the presence of DNA damage. In eukaryotes, Rad6- and Rad18-mediated PCNA ubiquitination at lysine 164 promotes recruitment of TLS polymerases, allowing cells to efficiently cope with DNA damage. However, several studies showed that TLS polymerases can be recruited also in the absence of PCNA ubiquitination. We hypothesized that the stability of the interactions between DNA polymerase δ (Pol δ) subunits and/or between Pol δ and PCNA at the primer/template junction is a crucial factor to determine the requirement of PCNA ubiquitination. To test this hypothesis, we used a structural mutant of Pol δ in which the interaction between Pol3 and Pol31 is inhibited. We found that in yeast, rad18Δ-associated UV hypersensitivity is suppressed by pol3-ct, a mutant allele of the POL3 gene that encodes the catalytic subunit of replicative Pol δ. pol3-ct suppressor effect was specifically dependent on the Rev1 and Pol ζ TLS polymerases. This result strongly suggests that TLS polymerases could rely much less on PCNA ubiquitination when Pol δ interaction with PCNA is partially compromised by mutations. In agreement with this model, we found that the pol3-FI allele suppressed rad18Δ-associated UV sensitivity as observed for pol3-ct. This POL3 allele carries mutations within a putative PCNA Interacting Peptide (PIP) motif. We then provided molecular and genetic evidence that this motif could contribute to Pol δ-PCNA interaction indirectly, although it is not a bona fide PIP. Overall, our results suggest that the primary role of PCNA ubiquitination is to allow TLS polymerases to outcompete Pol δ for PCNA access upon DNA damage. Replicative DNA polymerases have the essential role of replicating genomic DNA during the S phase of each cell cycle. DNA replication occurs smoothly and accurately if the DNA to be replicated is undamaged. Conversely, replicative DNA polymerases stall abruptly when they encounter a damaged base on their template. In this case, alternative specialized DNA polymerases are recruited to insert nucleotides at sites of base lesions. However, these translesion polymerases are not processive and they are poorly accurate. Therefore, they need to be tightly regulated. This is achieved by the covalent binding of the small ubiquitin peptide to the polymerase cofactor PCNA that subsequently triggers the recruitment of translesion polymerases at sites of DNA damage. Yet, recruitment of translesion polymerases independently of PCNA ubiquitination also has been documented, although the underlying mechanism is not known. Moreover, this observation makes more difficult to understand the exact role of PCNA ubiquitination. Here, we present strong genetic evidence in Saccharomyces cerevisiae implying that the replicative DNA polymerase δ (Pol δ) prevents the recruitment of the translesion polymerases Pol ζ and Rev1 following UV irradiation unless PCNA is ubiquitinated. Thus, the primary role of PCNA ubiquitination would be to allow translesion polymerases to outcompete Pol δ upon DNA damage. In addition, our results led us to propose that translesion polymerases could be recruited independently of PCNA ubiquitination when Pol δ association with PCNA is challenged, for instance at difficult-to-replicate loci.
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Baek IJ, Moss DS, Lustig AJ. The mre11 A470 alleles influence the hereditability and the segregation of telosomes in Saccharomyces cerevisiae. PLoS One 2017; 12:e0183549. [PMID: 28886051 PMCID: PMC5590830 DOI: 10.1371/journal.pone.0183549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 08/07/2017] [Indexed: 11/18/2022] Open
Abstract
Telomeres, the nucleoprotein complexes at the termini of linear chromosomes, are essential for the processes of end replication, end protection, and chromatin segregation. The Mre11 complex is involved in multiple cellular roles in DNA repair and structure in the regulation and function of telomere size homeostasis. In this study, we characterize yeast telomere chromatin structure, phenotypic heritability, and chromatin segregation in both wild-type [MRE11] and A470 motif alleles. MRE11 strains confer a telomere size of 300 base pairs of G+T irregular simple sequence repeats. This DNA and a portion of subtelomeric DNA is embedded in a telosome: a MNase-resistant non-nucleosomal particle. Chromatin immunoprecipitation shows a three to four-fold lower occupancy of Mre11A470T proteins than wild-type proteins in telosomes. Telosomes containing the Mre11A470T protein confer a greater resistance to MNase digestion than wild-type telosomes. The integration of a wild-type MRE11 allele into an ectopic locus in the genome of an mre11A470T mutant and the introduction of an mre11A470T allele at an ectopic site in a wild-type strain lead to unexpectedly differing results. In each case, the replicated sister chromatids inherit telosomes containing only the protein encoded by the genomic mre11 locus, even in the presence of protein encoded by the opposing ectopic allele. We hypothesize that the telosome segregates by a conservative mechanism. These data support a mechanism for the linkage between sister chromatid replication and maintenance of either identical mutant or identical wild-type telosomes after replication of sister chromatids. These data suggest the presence of an active mechanism for chromatin segregation in yeast.
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Affiliation(s)
- In-Joon Baek
- Department of Biochemistry and Molecular Biology, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - Daniel S. Moss
- Department of Biochemistry and Molecular Biology, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - Arthur J. Lustig
- Department of Biochemistry and Molecular Biology, Tulane University Medical Center, New Orleans, Louisiana, United States of America
- * E-mail:
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Mórocz M, Zsigmond E, Tóth R, Enyedi MZ, Pintér L, Haracska L. DNA-dependent protease activity of human Spartan facilitates replication of DNA-protein crosslink-containing DNA. Nucleic Acids Res 2017; 45:3172-3188. [PMID: 28053116 PMCID: PMC5389635 DOI: 10.1093/nar/gkw1315] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/22/2016] [Indexed: 01/24/2023] Open
Abstract
Mutations in SPARTAN are associated with early onset hepatocellular carcinoma and progeroid features. A regulatory function of Spartan has been implicated in DNA damage tolerance pathways such as translesion synthesis, but the exact function of the protein remained unclear. Here, we reveal the role of human Spartan in facilitating replication of DNA–protein crosslink-containing DNA. We found that purified Spartan has a DNA-dependent protease activity degrading certain proteins bound to DNA. In concert, Spartan is required for direct DPC removal in vivo; we also show that the protease Spartan facilitates repair of formaldehyde-induced DNA–protein crosslinks in later phases of replication using the bromodeoxyuridin (BrdU) comet assay. Moreover, DNA fibre assay indicates that formaldehyde-induced replication stress dramatically decreases the speed of replication fork movement in Spartan-deficient cells, which accumulate in the G2/M cell cycle phase. Finally, epistasis analysis mapped these Spartan functions to the RAD6-RAD18 DNA damage tolerance pathway. Our results reveal that Spartan facilitates replication of DNA–protein crosslink-containing DNA enzymatically, as a protease, which may explain its role in preventing carcinogenesis and aging.
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Affiliation(s)
- Mónika Mórocz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Eszter Zsigmond
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Róbert Tóth
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Márton Zs Enyedi
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Lajos Pintér
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
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31
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Jalal D, Chalissery J, Hassan AH. Genome maintenance in Saccharomyces cerevisiae: the role of SUMO and SUMO-targeted ubiquitin ligases. Nucleic Acids Res 2017; 45:2242-2261. [PMID: 28115630 PMCID: PMC5389695 DOI: 10.1093/nar/gkw1369] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/02/2017] [Indexed: 01/08/2023] Open
Abstract
The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyces cerevisiae have advanced our understanding of the DNA damage response, as well as the mechanisms the cell employs to maintain genome stability and how these mechanisms are regulated. Eukaryotic cells utilize post-translational modifications as a means for fine-tuning protein functions. Ubiquitylation and SUMOylation involve the attachment of small protein molecules onto proteins to modulate function or protein–protein interactions. SUMO in particular, was shown to act as a molecular glue when DNA damage occurs, facilitating the assembly of large protein complexes in repair foci. In other instances, SUMOylation alters a protein's biochemical activities, and interactions. SUMO-targeted ubiquitin ligases (STUbLs) are enzymes that target SUMOylated proteins for ubiquitylation and subsequent degradation, providing a function for the SUMO modification in the regulation and disassembly of repair complexes. Here, we discuss the major contributions of SUMO and STUbLs in the regulation of DNA damage repair pathways as well as in the maintenance of critical regions of the genome, namely rDNA regions, telomeres and the 2 μm circle in budding yeast.
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Affiliation(s)
- Deena Jalal
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
| | - Jisha Chalissery
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
| | - Ahmed H Hassan
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
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Huseinovic A, van Leeuwen JS, van Welsem T, Stulemeijer I, van Leeuwen F, Vermeulen NPE, Kooter JM, Vos JC. The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae. PLoS One 2017; 12:e0173573. [PMID: 28291796 PMCID: PMC5349473 DOI: 10.1371/journal.pone.0173573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/23/2017] [Indexed: 02/05/2023] Open
Abstract
Acetaminophen (APAP), although considered a safe drug, is one of the major causes of acute liver failure by overdose, and therapeutic chronic use can cause serious health problems. Although the reactive APAP metabolite N-acetyl-p-benzoquinoneimine (NAPQI) is clearly linked to liver toxicity, toxicity of APAP is also found without drug metabolism of APAP to NAPQI. To get more insight into mechanisms of APAP toxicity, a genome-wide screen in Saccharomyces cerevisiae for APAP-resistant deletion strains was performed. In this screen we identified genes related to the DNA damage response. Next, we investigated the link between genotype and APAP-induced toxicity or resistance by performing a more detailed screen with a library containing mutants of 1522 genes related to nuclear processes, like DNA repair and chromatin remodelling. We identified 233 strains that had an altered growth rate relative to wild type, of which 107 showed increased resistance to APAP and 126 showed increased sensitivity. Gene Ontology analysis identified ubiquitin homeostasis, regulation of transcription of RNA polymerase II genes, and the mitochondria-to-nucleus signalling pathway to be associated with APAP resistance, while histone exchange and modification, and vesicular transport were connected to APAP sensitivity. Indeed, we observed a link between ubiquitin levels and APAP resistance, whereby ubiquitin deficiency conferred resistance to APAP toxicity while ubiquitin overexpression resulted in sensitivity. The toxicity profile of various chemicals, APAP, and its positional isomer AMAP on a series of deletion strains with ubiquitin deficiency showed a unique resistance pattern for APAP. Furthermore, exposure to APAP increased the level of free ubiquitin and influenced the ubiquitination of proteins. Together, these results uncover a role for ubiquitin homeostasis in APAP-induced toxicity.
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Affiliation(s)
- Angelina Huseinovic
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jolanda S. van Leeuwen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jan M. Kooter
- AIMMS-Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, Amsterdam, The Netherlands
| | - J. Chris Vos
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Syed S, Desler C, Rasmussen LJ, Schmidt KH. A Novel Rrm3 Function in Restricting DNA Replication via an Orc5-Binding Domain Is Genetically Separable from Rrm3 Function as an ATPase/Helicase in Facilitating Fork Progression. PLoS Genet 2016; 12:e1006451. [PMID: 27923055 PMCID: PMC5140057 DOI: 10.1371/journal.pgen.1006451] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 10/31/2016] [Indexed: 11/21/2022] Open
Abstract
In response to replication stress cells activate the intra-S checkpoint, induce DNA repair pathways, increase nucleotide levels, and inhibit origin firing. Here, we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress. The N-terminal domain required for control of DNA synthesis maps to residues 186–212 that are also critical for binding Orc5 of the origin recognition complex. Deletion of this domain is lethal to cells lacking the replication checkpoint mediator Mrc1 and leads to mutations upon exposure to the replication stressor hydroxyurea. This novel Rrm3 function is independent of its established role as an ATPase/helicase in facilitating replication fork progression through polymerase blocking obstacles. Using quantitative mass spectrometry and genetic analyses, we find that the homologous recombination factor Rdh54 and Rad5-dependent error-free DNA damage bypass act as independent mechanisms on DNA lesions that arise when Rrm3 catalytic activity is disrupted whereas these mechanisms are dispensable for DNA damage tolerance when the replication function is disrupted, indicating that the DNA lesions generated by the loss of each Rrm3 function are distinct. Although both lesion types activate the DNA-damage checkpoint, we find that the resultant increase in nucleotide levels is not sufficient for continued DNA synthesis under replication stress. Together, our findings suggest a role of Rrm3, via its Orc5-binding domain, in restricting DNA synthesis that is genetically and physically separable from its established catalytic role in facilitating fork progression through replication blocks. When cells duplicate their genome, the replication machinery is constantly at risk of encountering obstacles, including unusual DNA structures, bound proteins, or transcribing polymerases and transcripts. Cells possess DNA helicases that facilitate movement of the replication fork through such obstacles. Here, we report the discovery that one of these DNA helicases, Rrm3, is also required for restricting DNA synthesis under replication stress. We find that the site in Rrm3 critical for this new replication function is also required for binding a subunit of the replication origin recognition complex, which raises the possibility that Rrm3 controls replication by affecting initiation. This is supported by our finding that Rrm3 associates with a subset of replication origins. Rrm3’s ability to restrict replication does not require its helicase activity or the phosphorylation site that regulates this activity. Notably, cells need error-free bypass pathways and homologous recombination to deal with DNA lesions that arise when the helicase function of Rrm3 is disrupted, but not when its replication function is disrupted. This indicates that the DNA lesions that form in the absence of the two distinct Rrm3 function are different, although both activate the DNA-damage checkpoint and are toxic to cells that lack the mediator of the replication checkpoint Mrc1.
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Affiliation(s)
- Salahuddin Syed
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
- Graduate Program in Cellular and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Claus Desler
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lene J. Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kristina H. Schmidt
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
- * E-mail:
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Toth A, Hegedus L, Juhasz S, Haracska L, Burkovics P. The DNA-binding box of human SPARTAN contributes to the targeting of Polη to DNA damage sites. DNA Repair (Amst) 2016; 49:33-42. [PMID: 27838458 DOI: 10.1016/j.dnarep.2016.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 11/16/2022]
Abstract
Inappropriate repair of UV-induced DNA damage results in human diseases such as Xeroderma pigmentosum (XP), which is associated with an extremely high risk of skin cancer. A variant form of XP is caused by the absence of Polη, which is normally able to bypass UV-induced DNA lesions in an error-free manner. However, Polη is highly error prone when replicating undamaged DNA and, thus, the regulation of the proper targeting of Polη is crucial for the prevention of mutagenesis and UV-induced cancer formation. Spartan is a novel regulator of the damage tolerance pathway, and its association with Ub-PCNA has a role in Polη targeting; however, our knowledge about its function is only rudimentary. Here, we describe a new biochemical property of purified human SPARTAN by showing that it is a DNA-binding protein. Using a DNA binding mutant, we provide in vivo evidence that DNA binding by SPARTAN regulates the targeting of Polη to damage sites after UV exposure, and this function contributes highly to its DNA-damage tolerance function.
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Affiliation(s)
- Agnes Toth
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lili Hegedus
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Szilvia Juhasz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Peter Burkovics
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
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Callegari AJ, Kelly TJ. Coordination of DNA damage tolerance mechanisms with cell cycle progression in fission yeast. Cell Cycle 2016; 15:261-73. [PMID: 26652183 PMCID: PMC5007584 DOI: 10.1080/15384101.2015.1121353] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA damage tolerance (DDT) mechanisms allow cells to synthesize a new DNA strand when the template is damaged. Many mutations resulting from DNA damage in eukaryotes are generated during DDT when cells use the mutagenic translesion polymerases, Rev1 and Polζ, rather than mechanisms with higher fidelity. The coordination among DDT mechanisms is not well understood. We used live-cell imaging to study the function of DDT mechanisms throughout the cell cycle of the fission yeast Schizosaccharomyces pombe. We report that checkpoint-dependent mitotic delay provides a cellular mechanism to ensure the completion of high fidelity DDT, largely by homology-directed repair (HDR). DDT by mutagenic polymerases is suppressed during the checkpoint delay by a mechanism dependent on Rad51 recombinase. When cells pass the G2/M checkpoint and can no longer delay mitosis, they completely lose the capacity for HDR and simultaneously exhibit a requirement for Rev1 and Polζ. Thus, DDT is coordinated with the checkpoint response so that the activity of mutagenic polymerases is confined to a vulnerable period of the cell cycle when checkpoint delay and HDR are not possible.
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Affiliation(s)
- A John Callegari
- a Molecular Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| | - Thomas J Kelly
- a Molecular Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
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Halmai M, Frittmann O, Szabo Z, Daraba A, Gali VK, Balint E, Unk I. Mutations at the Subunit Interface of Yeast Proliferating Cell Nuclear Antigen Reveal a Versatile Regulatory Domain. PLoS One 2016; 11:e0161307. [PMID: 27537501 PMCID: PMC4990258 DOI: 10.1371/journal.pone.0161307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/03/2016] [Indexed: 11/19/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) plays a key role in many cellular processes and due to that it interacts with a plethora of proteins. The main interacting surfaces of Saccharomyces cerevisiae PCNA have been mapped to the interdomain connecting loop and to the carboxy-terminal domain. Here we report that the subunit interface of yeast PCNA also has regulatory roles in the function of several DNA damage response pathways. Using site-directed mutagenesis we engineered mutations at both sides of the interface and investigated the effect of these alleles on DNA damage response. Genetic experiments with strains bearing the mutant alleles revealed that mutagenic translesion synthesis, nucleotide excision repair, and homologous recombination are all regulated through residues at the subunit interface. Moreover, genetic characterization of one of our mutants identifies a new sub-branch of nucleotide excision repair. Based on these results we conclude that residues at the subunit boundary of PCNA are not only important for the formation of the trimer structure of PCNA, but they constitute a regulatory protein domain that mediates different DNA damage response pathways, as well.
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Affiliation(s)
- Miklos Halmai
- The Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Orsolya Frittmann
- The Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltan Szabo
- The Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Andreea Daraba
- The Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Vamsi K. Gali
- The Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Eva Balint
- The Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ildiko Unk
- The Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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PCNA SUMOylation protects against PCNA polyubiquitination-mediated, Rad59-dependent, spontaneous, intrachromosomal gene conversion. Mutat Res 2016; 791-792:10-18. [PMID: 27505077 DOI: 10.1016/j.mrfmmm.2016.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/29/2016] [Accepted: 08/01/2016] [Indexed: 11/23/2022]
Abstract
Homologous recombination is crucial in both the maintenance of genome stability and the generation of genetic diversity. Recently, multiple aspects of the recombination machinery functioning at arrested DNA replication forks have been established, yet the roles of diverse modifications of PCNA, the key platform organizing the replication complex, in intrachromosomal recombination have not been comprehensively elucidated. Here, we report how PCNA SUMOylation and/or polyubiquitination affects recombination between direct repeats in S. cerevisiae. Our results show that these PCNA modifications primarily affect gene conversion, whereas their effect on the recombination-mediated deletion of intervening sequence is much less obvious. Siz1-dependent PCNA SUMOylation strongly limits Rad52/Rad51/Rad59-dependent gene conversion. A 5- to 10-fold increase in the frequency of such recombination events is observed in Siz1-defective strains, but this increase is fully suppressed when PCNA polyubiquitination is also compromised. PCNA polyubiquitination can stimulate gene conversion in both PCNA SUMOylation-proficient and SUMOylation-deficient strains. On the other hand, in PCNA polyubiquitination-deficient strains, the lack of PCNA SUMOylation does not affect GC levels. Therefore, we postulate that the antirecombinogenic activity of Siz1 mainly concerns recombination induced by PCNA polyubiquitination. In the absence of PCNA SUMOylation, the frequency of PCNA polyubiquitination-mediated gene conversion is not only increased, but it is also channeled into the Rad59-dependent pathway. Additionally, we show a weak inhibitory effect of Rad5 on Rad52/Rad59-directed single-strand annealing.
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Abstract
Viruses often interfere with the DNA damage response to better replicate in their hosts. The human immunodeficiency virus 1 (HIV-1) viral protein R (Vpr) protein has been reported to modulate the activity of the DNA repair structure-specific endonuclease subunit (SLX4) complex and to promote cell cycle arrest. Vpr also interferes with the base-excision repair pathway by antagonizing the uracil DNA glycosylase (Ung2) enzyme. Using an unbiased quantitative proteomic screen, we report that Vpr down-regulates helicase-like transcription factor (HLTF), a DNA translocase involved in the repair of damaged replication forks. Vpr subverts the DDB1-cullin4-associated-factor 1 (DCAF1) adaptor of the Cul4A ubiquitin ligase to trigger proteasomal degradation of HLTF. This event takes place rapidly after Vpr delivery to cells, before and independently of Vpr-mediated G2 arrest. HLTF is degraded in lymphocytic cells and macrophages infected with Vpr-expressing HIV-1. Our results reveal a previously unidentified strategy for HIV-1 to antagonize DNA repair in host cells.
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Kobayashi S, Keka IS, Guilbaud G, Sale J, Narita T, Abdel-Aziz HI, Wang X, Ogawa S, Sasanuma H, Chiu R, Oestergaard VH, Lisby M, Takeda S. The role of HERC2 and RNF8 ubiquitin E3 ligases in the promotion of translesion DNA synthesis in the chicken DT40 cell line. DNA Repair (Amst) 2016; 40:67-76. [PMID: 26994443 DOI: 10.1016/j.dnarep.2016.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/12/2016] [Accepted: 02/03/2016] [Indexed: 12/20/2022]
Abstract
The replicative DNA polymerases are generally blocked by template DNA damage. The resulting replication arrest can be released by one of two post-replication repair (PRR) pathways, translesion DNA synthesis (TLS) and template switching by homologous recombination (HR). The HERC2 ubiquitin ligase plays a role in homologous recombination by facilitating the assembly of the Ubc13 ubiquitin-conjugating enzyme with the RNF8 ubiquitin ligase. To explore the role of HERC2 and RNF8 in PRR, we examined immunoglobulin diversification in chicken DT40 cells deficient in HERC2 and RNF8. Unexpectedly, the HERC2(-/-) and RNF8(-/-) cells and HERC2(-/-)/RNF8(-/-) double mutant cells exhibit a significant reduction in the rate of immunoglobulin (Ig) hypermutation, compared to wild-type cells. Further, the HERC2(-/-) and RNF8(-/-) mutants exhibit defective maintenance of replication fork progression immediately after exposure to UV while retaining proficient post-replicative gap filling. These mutants are both proficient in mono-ubiquitination of PCNA. Taken together, these results suggest that HERC2 and RNF8 promote TLS past abasic sites and UV-lesions at or very close to stalled replication forks.
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Affiliation(s)
- Shunsuke Kobayashi
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Islam Shamima Keka
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Guillaume Guilbaud
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Julian Sale
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Takeo Narita
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - H Ismail Abdel-Aziz
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan; Faculty of Medicine, Seuz Canal University, circular road Ez-Eldeen, Ismailia 41522, Egypt
| | - Xin Wang
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Saki Ogawa
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Roland Chiu
- University College Groningen, University of Groningen, 9718 BG Groningen, Hoendiepskade 23-24, The Netherlands
| | - Vibe H Oestergaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan.
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40
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Burkovics P, Dome L, Juhasz S, Altmannova V, Sebesta M, Pacesa M, Fugger K, Sorensen CS, Lee MYWT, Haracska L, Krejci L. The PCNA-associated protein PARI negatively regulates homologous recombination via the inhibition of DNA repair synthesis. Nucleic Acids Res 2016; 44:3176-89. [PMID: 26792895 PMCID: PMC4838361 DOI: 10.1093/nar/gkw024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/08/2016] [Indexed: 12/13/2022] Open
Abstract
Successful and accurate completion of the replication of damage-containing DNA requires mainly recombination and RAD18-dependent DNA damage tolerance pathways. RAD18 governs at least two distinct mechanisms: translesion synthesis (TLS) and template switching (TS)-dependent pathways. Whereas TS is mainly error-free, TLS can work in an error-prone manner and, as such, the regulation of these pathways requires tight control to prevent DNA errors and potentially oncogenic transformation and tumorigenesis. In humans, the PCNA-associated recombination inhibitor (PARI) protein has recently been shown to inhibit homologous recombination (HR) events. Here, we describe a biochemical mechanism in which PARI functions as an HR regulator after replication fork stalling and during double-strand break repair. In our reconstituted biochemical system, we show that PARI inhibits DNA repair synthesis during recombination events in a PCNA interaction-dependent way but independently of its UvrD-like helicase domain. In accordance, we demonstrate that PARI inhibits HR in vivo, and its knockdown suppresses the UV sensitivity of RAD18-depleted cells. Our data reveal a novel human regulatory mechanism that limits the extent of HR and represents a new potential target for anticancer therapy.
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Affiliation(s)
- Peter Burkovics
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, 6726 Szeged, Hungary Department of Biology, Masaryk University, 625 00 Brno, Czech Republic
| | - Lili Dome
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Szilvia Juhasz
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | | | - Marek Sebesta
- Department of Biology, Masaryk University, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, 625 00 Brno, Czech Republic International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St Anne's University Hospital Brno, 656 91 Brno, Czech Republic
| | - Martin Pacesa
- Department of Biology, Masaryk University, 625 00 Brno, Czech Republic
| | - Kasper Fugger
- Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, 10595 NY, USA
| | - Lajos Haracska
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Lumir Krejci
- Department of Biology, Masaryk University, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, 625 00 Brno, Czech Republic International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St Anne's University Hospital Brno, 656 91 Brno, Czech Republic
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41
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Achar YJ, Balogh D, Neculai D, Juhasz S, Morocz M, Gali H, Dhe-Paganon S, Venclovas Č, Haracska L. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling. Nucleic Acids Res 2015; 43:10277-91. [PMID: 26350214 PMCID: PMC4666394 DOI: 10.1093/nar/gkv896] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/27/2015] [Indexed: 12/13/2022] Open
Abstract
Defects in the ability to respond properly to an unrepaired DNA lesion blocking replication promote genomic instability and cancer. Human HLTF, implicated in error-free replication of damaged DNA and tumour suppression, exhibits a HIRAN domain, a RING domain, and a SWI/SNF domain facilitating DNA-binding, PCNA-polyubiquitin-ligase, and dsDNA-translocase activities, respectively. Here, we investigate the mechanism of HLTF action with emphasis on its HIRAN domain. We found that in cells HLTF promotes the filling-in of gaps left opposite damaged DNA during replication, and this postreplication repair function depends on its HIRAN domain. Our biochemical assays show that HIRAN domain mutant HLTF proteins retain their ubiquitin ligase, ATPase and dsDNA translocase activities but are impaired in binding to a model replication fork. These data and our structural study indicate that the HIRAN domain recruits HLTF to a stalled replication fork, and it also provides the direction for the movement of the dsDNA translocase motor domain for fork reversal. In more general terms, we suggest functional similarities between the HIRAN, the OB, the HARP2, and other domains found in certain motor proteins, which may explain why only a subset of DNA translocases can carry out fork reversal.
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Affiliation(s)
- Yathish Jagadheesh Achar
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - David Balogh
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Dante Neculai
- Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Szilvia Juhasz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Monika Morocz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Himabindu Gali
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue - LC-3310, Boston, MA 02215, USA
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
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42
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Abstract
Human lymphoid malignancies inherit gene expression networks from their normal B-cell counterpart and co-opt them for their own oncogenic purpose, which is usually governed by transcription factors and signaling pathways. These transcription factors and signaling pathways are precisely regulated at multiple steps, including ubiquitin modification. Protein ubiqutination plays a role in almost all cellular events and in many human diseases. In the past few years, multiple studies have expanded the role of ubiquitination in the genesis of diverse lymphoid malignancies. Here, we discuss our current understanding of both proteolytic and non-proteolytic functions of the protein ubiquitination system and describe how it is involved in the pathogenesis of human lymphoid cancers. Lymphoid-restricted ubiquitination mechanisms, including ubiquitin E3 ligases and deubiquitinating enzymes, provide great opportunities for the development of targeted therapies for lymphoid cancers.
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Affiliation(s)
- Yibin Yang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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43
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Yin Y, Petes TD. Recombination between homologous chromosomes induced by unrepaired UV-generated DNA damage requires Mus81p and is suppressed by Mms2p. PLoS Genet 2015; 11:e1005026. [PMID: 25738287 PMCID: PMC4349867 DOI: 10.1371/journal.pgen.1005026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/25/2015] [Indexed: 11/18/2022] Open
Abstract
DNA lesions caused by UV radiation are highly recombinogenic. In wild-type cells, the recombinogenic effect of UV partially reflects the processing of UV-induced pyrimidine dimers into DNA gaps or breaks by the enzymes of the nucleotide excision repair (NER) pathway. In this study, we show that unprocessed pyrimidine dimers also potently induce recombination between homologs. In NER-deficient rad14 diploid strains, we demonstrate that unexcised pyrimidine dimers stimulate crossovers, noncrossovers, and break-induced replication events. The same dose of UV is about six-fold more recombinogenic in a repair-deficient strain than in a repair-proficient strain. We also examined the roles of several genes involved in the processing of UV-induced damage in NER-deficient cells. We found that the resolvase Mus81p is required for most of the UV-induced inter-homolog recombination events. This requirement likely reflects the Mus81p-associated cleavage of dimer-blocked replication forks. The error-free post-replication repair pathway mediated by Mms2p suppresses dimer-induced recombination between homologs, possibly by channeling replication-blocking lesions into recombination between sister chromatids. Ultraviolet (UV) light is a ubiquitous agent of exogenous DNA damage. In normal cells, the nucleotide excision repair (NER) pathway is the primary mechanism for repair of UV-induced DNA lesions. Defects in the NER pathway are associated with the human disease xeroderma pigmentosum (XP), and XP patients are prone to skin cancer. Mitotic recombination is strongly stimulated by UV treatment. In this study, we examined whether such stimulation requires the NER pathway. We show that, in the absence of NER, UV is still able to greatly induce recombination. We then characterized a nuclease that is required to generate recombinogenic breaks. Finally, we examined a previously known recombinogenic pathway called the “post-replication repair (PRR) pathway.” Our results suggest that the PRR pathway mainly promotes recombination between sister chromatids, and suppresses recombination between chromosome homologs.
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Affiliation(s)
- Yi Yin
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Thomas D. Petes
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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44
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Prado F. Homologous recombination maintenance of genome integrity during DNA damage tolerance. Mol Cell Oncol 2014; 1:e957039. [PMID: 27308329 PMCID: PMC4905194 DOI: 10.4161/23723548.2014.957039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023]
Abstract
The DNA strand exchange protein Rad51 provides a safe mechanism for the repair of DNA breaks using the information of a homologous DNA template. Homologous recombination (HR) also plays a key role in the response to DNA damage that impairs the advance of the replication forks by providing mechanisms to circumvent the lesion and fill in the tracks of single-stranded DNA that are generated during the process of lesion bypass. These activities postpone repair of the blocking lesion to ensure that DNA replication is completed in a timely manner. Experimental evidence generated over the last few years indicates that HR participates in this DNA damage tolerance response together with additional error-free (template switch) and error-prone (translesion synthesis) mechanisms through intricate connections, which are presented here. The choice between repair and tolerance, and the mechanism of tolerance, is critical to avoid increased mutagenesis and/or genome rearrangements, which are both hallmarks of cancer.
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Affiliation(s)
- Félix Prado
- Departamento de Biología Molecular; Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) ; Consejo Superior de Investigaciones Científicas (CSIC) ; Seville, Spain
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45
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Visualization of recombination-mediated damage bypass by template switching. Nat Struct Mol Biol 2014; 21:884-92. [PMID: 25195051 PMCID: PMC4189914 DOI: 10.1038/nsmb.2888] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 08/13/2014] [Indexed: 12/29/2022]
Abstract
Template switching (TS) mediates damage-bypass via a recombination-related mechanism involving PCNA polyubiquitylation and Polymerase δ-dependent DNA synthesis. Using two-dimensional gel electrophoresis and electron microscopy, here we characterize TS intermediates arising in Saccharomyces cerevisiae at a defined chromosome locus, identifying five major families of intermediates. Single-stranded DNA gaps in the range of 150-200 nucleotides, and not DNA ends, initiate TS by strand invasion. This causes re-annealing of the parental strands and exposure of the non-damaged newly synthesized chromatid as template for replication by the other blocked nascent strand. Structures resembling double Holliday Junctions, postulated to be central double-strand break repair intermediates, but so far only visualized in meiosis, mediate late stages of TS, before being processed to hemicatenanes. Our results reveal the DNA transitions accounting for recombination-mediated DNA damage tolerance in mitotic cells and for replication under conditions of genotoxic stress.
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46
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Kramarz K, Litwin I, Cal-Bąkowska M, Szakal B, Branzei D, Wysocki R, Dziadkowiec D. Swi2/Snf2-like protein Uls1 functions in the Sgs1-dependent pathway of maintenance of rDNA stability and alleviation of replication stress. DNA Repair (Amst) 2014; 21:24-35. [PMID: 25091157 DOI: 10.1016/j.dnarep.2014.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 05/05/2014] [Accepted: 05/25/2014] [Indexed: 10/25/2022]
Abstract
The Saccharomyces cerevisiae Uls1 belongs to the Swi2/Snf2 family of DNA-dependent ATPases and a new protein family of SUMO-targeted ubiquitin ligases. Here we show that Uls1 is implicated in DNA repair independently of the replication stress response pathways mediated by the endonucleases Mus81 and Yen1 and the helicases Mph1 and Srs2. Uls1 works together with Sgs1 and we demonstrate that the attenuation of replication stress-related defects in sgs1Δ by deletion of ULS1 depends on a functional of Rad51 recombinase and post-replication repair pathway mediated by Rad18 and Rad5, but not on the translesion polymerase, Rev3. The higher resistance of sgs1Δ uls1Δ mutants to genotoxic stress compared to single sgs1Δ cells is not the result of decreased formation or accelerated resolution of recombination-dependent DNA structures. Instead, deletion of ULS1 restores stability of the rDNA region in sgs1Δ cells. Our data suggest that Uls1 may contribute to genomic stability during DNA synthesis and channel the repair of replication lesions into the Sgs1-dependent pathway, with DNA translocase and SUMO binding activities of Uls1 as well as a RING domain being essential for its functions in replication stress response.
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Affiliation(s)
- Karol Kramarz
- Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, 50-328 Wrocław, Poland
| | - Ireneusz Litwin
- Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, 50-328 Wrocław, Poland
| | - Magdalena Cal-Bąkowska
- Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, 50-328 Wrocław, Poland
| | - Barnabas Szakal
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, Milan 20139, Italy
| | - Dana Branzei
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, Milan 20139, Italy
| | - Robert Wysocki
- Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, 50-328 Wrocław, Poland
| | - Dorota Dziadkowiec
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland.
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47
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Gonzalez-Huici V, Szakal B, Urulangodi M, Psakhye I, Castellucci F, Menolfi D, Rajakumara E, Fumasoni M, Bermejo R, Jentsch S, Branzei D. DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity. EMBO J 2014; 33:327-40. [PMID: 24473148 PMCID: PMC3983681 DOI: 10.1002/embj.201387425] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.
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48
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Abstract
DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.
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49
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Burkovics P, Sebesta M, Balogh D, Haracska L, Krejci L. Strand invasion by HLTF as a mechanism for template switch in fork rescue. Nucleic Acids Res 2013; 42:1711-20. [PMID: 24198246 PMCID: PMC3919600 DOI: 10.1093/nar/gkt1040] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Stalling of replication forks at unrepaired DNA lesions can result in discontinuities opposite the damage in the newly synthesized DNA strand. Translesion synthesis or facilitating the copy from the newly synthesized strand of the sister duplex by template switching can overcome such discontinuities. During template switch, a new primer–template junction has to be formed and two mechanisms, including replication fork reversal and D-loop formation have been suggested. Genetic evidence indicates a major role for yeast Rad5 in template switch and that both Rad5 and its human orthologue, Helicase-like transcription factor (HLTF), a potential tumour suppressor can facilitate replication fork reversal. This study demonstrates the ability of HLTF and Rad5 to form a D-loop without requiring ATP binding and/or hydrolysis. We also show that this strand-pairing activity is independent of RAD51 in vitro and is not mechanistically related to that of another member of the SWI/SNF family, RAD54. In addition, the 3′-end of the invading strand in the D-loop can serve as a primer and is extended by DNA polymerase. Our data indicate that HLTF is involved in a RAD51-independent D-loop branch of template switch pathway that can promote repair of gaps formed during replication of damaged DNA.
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Affiliation(s)
- Peter Burkovics
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, HU-6726 Szeged, Hungary, Department of Biology, Masaryk University, Brno, Czech Republic, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic and International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, CZ-62500 Brno, Czech Republic
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50
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Mórocz M, Gali H, Raskó I, Downes CS, Haracska L. Single cell analysis of human RAD18-dependent DNA post-replication repair by alkaline bromodeoxyuridine comet assay. PLoS One 2013; 8:e70391. [PMID: 23936422 PMCID: PMC3735594 DOI: 10.1371/journal.pone.0070391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/19/2013] [Indexed: 01/02/2023] Open
Abstract
Damage to DNA can block replication progression resulting in gaps in the newly synthesized DNA. Cells utilize a number of post-replication repair (PRR) mechanisms such as the RAD18 controlled translesion synthesis or template switching to overcome the discontinuities formed opposite the DNA lesions and to complete DNA replication. Gaining more insights into the role of PRR genes promotes better understanding of DNA damage tolerance and of how their malfunction can lead to increased genome instability and cancer. However, a simple and efficient method to characterise gene specific PRR deficiencies at a single cell level has not been developed. Here we describe the so named BrdU comet PRR assay to test the contribution of human RAD18 to PRR at a single cell level, by which we kinetically characterized the consequences of the deletion of human RAD18 on the replication of UV-damaged DNA. Moreover, we demonstrate the capability of our method to evaluate PRR at a single cell level in unsynchronized cell population.
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Affiliation(s)
- Mónika Mórocz
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - Himabindu Gali
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - István Raskó
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - C. Stephen Downes
- Biomedical Sciences Research Institute, School of Biomedical Sciences, University of Ulster, Coleraine, Londonderry, Northern Ireland
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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