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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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Pekker E, Priskin K, Szabó-Kriston É, Csányi B, Buzás-Bereczki O, Adorján L, Szukacsov V, Pintér L, Rusvai M, Cooper P, Kiss-Tóth E, Haracska L. Development of a Large-Scale Pathogen Screening Test for the Biosafety Evaluation of Canine Mesenchymal Stem Cells. Biol Proced Online 2023; 25:33. [PMID: 38097939 PMCID: PMC10720183 DOI: 10.1186/s12575-023-00226-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The action of mesenchymal stem cells (MSCs) is the subject of intense research in the field of regenerative medicine, including their potential use in companion animals, such as dogs. To ensure the safety of canine MSC batches for their application in regenerative medicine, a quality control test must be conducted in accordance with Good Manufacturing Practices (GMP). Based on guidance provided by the European Medicines Agency, this study aimed to develop and validate a highly sensitive and robust, nucleic acid-based test panel for the detection of various canine pathogens. Analytical sensitivity, specificity, amplification efficiency, and linearity were evaluated to ensure robust assessment. Additionally, viable spike-in controls were used to control for optimal nucleic acid extraction. The conventional PCR-based and real-time PCR-based pathogen assays were evaluated in a real-life setting, by direct testing MSC batches. RESULTS The established nucleic acid-based assays displayed remarkable sensitivity, detecting 100-1 copies/reaction of template DNA. They also exhibited high specificity and efficiency. Moreover, highly effective nucleic acid isolation was confirmed by the sensitive detection of spike-in controls. The detection capacity of our optimized and validated methods was determined by direct pathogen testing of nine MSC batches that displayed unusual phenotypes, such as reduced cell division or other deviating characteristics. Among these MCS batches of uncertain purity, only one tested negative for all pathogens. The direct testing of these samples yielded positive results for important canine pathogens, including tick-borne disease-associated species and viral members of the canine infectious respiratory disease complex (CIRDC). Notably, samples positive for the etiological agents responsible for enteritis (CPV), leptospirosis (Leptospira interrogans), and neosporosis (Neospora caninum) were also identified. Furthermore, we conducted biosafety evaluation of 12 MSC batches intended for therapeutic application. Eleven MSC batches were found to be free of extraneous agents, and only one tested positive for a specific pathogen, namely, canine parvovirus. CONCLUSION In this study, we established and validated reliable, highly sensitive, and accurate nucleic acid-based testing methods for a broad spectrum of canine pathogens.
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Affiliation(s)
- Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, H-6726, Hungary
- Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, Szeged, H-6720, Hungary
- Delta Bio 2000 Ltd., Szeged, H-6726, Hungary
| | | | | | | | | | | | - Valéria Szukacsov
- HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, H-6726, Hungary
| | | | | | | | - Endre Kiss-Tóth
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, S10 2RX, Sheffield, UK
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, H-6726, Hungary.
- Delta Bio 2000 Ltd., Szeged, H-6726, Hungary.
- National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117, Budapest, Hungary.
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Fenteany G, Sharma G, Gaur P, Borics A, Wéber E, Kiss E, Haracska L. A series of xanthenes inhibiting Rad6 function and Rad6-Rad18 interaction in the PCNA ubiquitination cascade. iScience 2022; 25:104053. [PMID: 35355521 PMCID: PMC8958325 DOI: 10.1016/j.isci.2022.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitination of proliferating cell nuclear antigen (PCNA) triggers pathways of DNA damage tolerance, including mutagenic translesion DNA synthesis, and comprises a cascade of reactions involving the E1 ubiquitin-activating enzyme Uba1, the E2 ubiquitin-conjugating enzyme Rad6, and the E3 ubiquitin ligase Rad18. We report here the discovery of a series of xanthenes that inhibit PCNA ubiquitination, Rad6∼ubiquitin thioester formation, and the Rad6–Rad18 interaction. Structure-activity relationship experiments across multiple assays reveal chemical and structural features important for different activities along the pathway to PCNA ubiquitination. The compounds that inhibit these processes are all a subset of the xanthen-3-ones we tested. These small molecules thus represent first-in-class probes of Rad6 function and the association of Rad6 and Rad18, the latter being a new inhibitory activity discovered for a small molecule, in the PCNA ubiquitination cascade and potential therapeutic agents to contain cancer progression. Alpha-based HTS for PCNA ubiquitination modulators Target-based characterization of hits A series of xanthenes that inhibit Rad6 functions and Rad6–Rad18 interaction
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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: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Majoros H, Borsos BN, Ujfaludi Z, Páhi ZG, Mórocz M, Haracska L, Boros IM, Pankotai T. SerpinB10, a Serine Protease Inhibitor, Is Implicated in UV-Induced Cellular Response. Int J Mol Sci 2021; 22:ijms22168500. [PMID: 34445206 PMCID: PMC8395218 DOI: 10.3390/ijms22168500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022] Open
Abstract
UV-induced DNA damage response and repair are extensively studied processes, as any malfunction in these pathways contributes to the activation of tumorigenesis. Although several proteins involved in these cellular mechanisms have been described, the entire repair cascade has remained unexplored. To identify new players in UV-induced repair, we performed a microarray screen, in which we found SerpinB10 (SPB10, Bomapin) as one of the most dramatically upregulated genes following UV irradiation. Here, we demonstrated that an increased mRNA level of SPB10 is a general cellular response following UV irradiation regardless of the cell type. We showed that although SPB10 is implicated in the UV-induced cellular response, it has no indispensable function in cell survival upon UV irradiation. Nonetheless, we revealed that SPB10 might be involved in delaying the duration of DNA repair in interphase and also in S-phase cells. Additionally, we also highlighted the interaction between SPB10 and H3. Based on our results, it seems that SPB10 protein is implicated in UV-induced stress as a “quality control protein”, presumably by slowing down the repair process.
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Affiliation(s)
- Hajnalka Majoros
- Institute of Pathology, Faculty of Medicine, University of Szeged, 1 Állomás utca, H-6725 Szeged, Hungary; (H.M.); (B.N.B.); (Z.U.); (Z.G.P.)
| | - Barbara N. Borsos
- Institute of Pathology, Faculty of Medicine, University of Szeged, 1 Állomás utca, H-6725 Szeged, Hungary; (H.M.); (B.N.B.); (Z.U.); (Z.G.P.)
| | - Zsuzsanna Ujfaludi
- Institute of Pathology, Faculty of Medicine, University of Szeged, 1 Állomás utca, H-6725 Szeged, Hungary; (H.M.); (B.N.B.); (Z.U.); (Z.G.P.)
| | - Zoltán G. Páhi
- Institute of Pathology, Faculty of Medicine, University of Szeged, 1 Állomás utca, H-6725 Szeged, Hungary; (H.M.); (B.N.B.); (Z.U.); (Z.G.P.)
| | - Mónika Mórocz
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, H-6726 Szeged, Hungary; (M.M.); (L.H.)
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, H-6726 Szeged, Hungary; (M.M.); (L.H.)
| | - Imre Miklós Boros
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - Tibor Pankotai
- Institute of Pathology, Faculty of Medicine, University of Szeged, 1 Állomás utca, H-6725 Szeged, Hungary; (H.M.); (B.N.B.); (Z.U.); (Z.G.P.)
- Correspondence: ; Tel.: +36-62-546-164
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Priskin K, Pólya S, Pintér L, Jaksa G, Csányi B, Enyedi MZ, Sági-Zsigmond E, Sükösd F, Oláh-Németh O, Kelemen G, Nikolényi A, Uhercsák G, Sántha D, Dobi Á, Szilágyi É, Valicsek E, Tordai L, Tóth R, Kahán Z, Haracska L. BC-Monitor: Towards a Routinely Accessible Circulating Tumor DNA-Based Tool for Real-Time Monitoring Breast Cancer Progression and Treatment Effectiveness. Cancers (Basel) 2021; 13:3489. [PMID: 34298704 PMCID: PMC8305126 DOI: 10.3390/cancers13143489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is increasingly employed in the screening, follow-up, and monitoring of the continuously evolving tumor; however, most ctDNA assays validated for clinical use cannot maintain the right balance between sensitivity, coverage, sample requirements, time, and cost. Here, we report our BC-monitor, a simple, well-balanced ctDNA diagnostic approach using a gene panel significant in breast cancer and an optimized multiplex PCR-based NGS protocol capable of identifying allele variant frequencies below 1% in cell-free plasma DNA. We monitored a cohort of 45 breast cancer patients prospectively enrolled into our study receiving neoadjuvant chemotherapy or endocrine therapy or palliative therapy for metastatic diseases. Their tumor mutation status was examined in the archived tumor samples and plasma samples collected before and continuously during therapy. Traceable mutations of the used 38-plex NGS assay were found in approximately two-thirds of the patients. Importantly, we detected new pathogenic variants in follow-up plasma samples that were not detected in the primary tumor and baseline plasma samples. We proved that the BC-monitor can pre-indicate disease progression four-six months earlier than conventional methods. Our study highlights the need for well-designed ctDNA monitoring during treatment and follow-up, integrated into a real-time treatment assessment, which could provide information on the active tumor DNA released into the blood.
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Affiliation(s)
- Katalin Priskin
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Sára Pólya
- Visal Plus Ltd., 6726 Szeged, Hungary; (S.P.); (B.C.)
| | - Lajos Pintér
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Gábor Jaksa
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | | | - Márton Zsolt Enyedi
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Eszter Sági-Zsigmond
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Farkas Sükösd
- Department of Pathology, University of Szeged, 6701 Szeged, Hungary;
| | - Orsolya Oláh-Németh
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Gyöngyi Kelemen
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Alíz Nikolényi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Gabriella Uhercsák
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Dóra Sántha
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Ágnes Dobi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Éva Szilágyi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Erzsébet Valicsek
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - László Tordai
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Rozália Tóth
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Zsuzsanna Kahán
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Biological Research Centre, Institute of Genetics, 6726 Szeged, Hungary
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Li Q, Dudás K, Tick G, Haracska L. Coordinated Cut and Bypass: Replication of Interstrand Crosslink-Containing DNA. Front Cell Dev Biol 2021; 9:699966. [PMID: 34262911 PMCID: PMC8275186 DOI: 10.3389/fcell.2021.699966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
DNA interstrand crosslinks (ICLs) are covalently bound DNA lesions, which are commonly induced by chemotherapeutic drugs, such as cisplatin and mitomycin C or endogenous byproducts of metabolic processes. This type of DNA lesion can block ongoing RNA transcription and DNA replication and thus cause genome instability and cancer. Several cellular defense mechanism, such as the Fanconi anemia pathway have developed to ensure accurate repair and DNA replication when ICLs are present. Various structure-specific nucleases and translesion synthesis (TLS) polymerases have come into focus in relation to ICL bypass. Current models propose that a structure-specific nuclease incision is needed to unhook the ICL from the replication fork, followed by the activity of a low-fidelity TLS polymerase enabling replication through the unhooked ICL adduct. This review focuses on how, in parallel with the Fanconi anemia pathway, PCNA interactions and ICL-induced PCNA ubiquitylation regulate the recruitment, substrate specificity, activity, and coordinated action of certain nucleases and TLS polymerases in the execution of stalled replication fork rescue via ICL bypass.
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Affiliation(s)
- Qiuzhen Li
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Kata Dudás
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Hungary
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Kriston-Pál É, Haracska L, Cooper P, Kiss-Tóth E, Szukacsov V, Monostori É. A Regenerative Approach to Canine Osteoarthritis Using Allogeneic, Adipose-Derived Mesenchymal Stem Cells. Safety Results of a Long-Term Follow-Up. Front Vet Sci 2020; 7:510. [PMID: 32903517 PMCID: PMC7438407 DOI: 10.3389/fvets.2020.00510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/03/2020] [Indexed: 01/11/2023] Open
Abstract
Mesenchymal stem cells (MSC) are emerging as an effective therapeutic tool in treating canine osteoarthritis (OA). In this report, we focused on the questions of whether MSC transplantation has long-term beneficial effects for the improvement in motion and also evaluated the safety of MSC injection. Visceral adipose tissue, a surgical waste obtained during routine ovariectomy served as a source of allogeneic MSCs and used to treat OA. Altogether, fifty-eight dogs were transplanted in the study suffering from OA in the elbow (42 animals), hip (5), knee (8), ankle (2), and hock (1). The effect of MSC transplantation was evaluated by the degree of lameness at a 4-5-years follow-up period based on the owners' subjective observations. The results showed that 83% of the OA patients improved or retained improvement in lameness. Clinical safety of the treatment was assessed by evaluating the coincidence of tumors or other diseases and other adverse reactions (such as local inflammation) after MSC cell therapy. Two incidences of local inflammation for <1 week at the site of injection were reported. No other adverse reactions were detected post-treatment. Sixteen dogs died during the study, 4 due to cancer and 12 due to other diseases, diagnosed by veterinarians. Overall, our survey suggests that MSC transplantation has long-term beneficial effects in reducing lameness. Moreover, no enrichment in a specific cause of death was observed in the transplanted animals, compared to reported literature. Our data suggest that MSC treatment could be an effective and safe long-term therapy for canine OA.
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Affiliation(s)
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Paul Cooper
- Assentra Limited, Chelmsford, United Kingdom
| | - Endre Kiss-Tóth
- University of Sheffield, Department of Infection, Immunity & Cardiovascular Disease, Sheffield, United Kingdom
| | | | - Éva Monostori
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
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Fenteany G, Gaur P, Sharma G, Pintér L, Kiss E, Haracska L. Robust high-throughput assays to assess discrete steps in ubiquitination and related cascades. BMC Mol Cell Biol 2020; 21:21. [PMID: 32228444 PMCID: PMC7106726 DOI: 10.1186/s12860-020-00262-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/12/2020] [Indexed: 01/21/2023] Open
Abstract
Background Ubiquitination and ubiquitin-like protein post-translational modifications play an enormous number of roles in cellular processes. These modifications are constituted of multistep reaction cascades. Readily implementable and robust methods to evaluate each step of the overall process, while presently limited, are critical to the understanding and modulation of the reaction sequence at any desired level, both in terms of basic research and potential therapeutic drug discovery and development. Results We developed multiple robust and reliable high-throughput assays to interrogate each of the sequential discrete steps in the reaction cascade leading to protein ubiquitination. As models for the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzyme, the E3 ubiquitin ligase, and their ultimate substrate of ubiquitination in a cascade, we examined Uba1, Rad6, Rad18, and proliferating cell nuclear antigen (PCNA), respectively, in reconstituted systems. Identification of inhibitors of this pathway holds promise in cancer therapy since PCNA ubiquitination plays a central role in DNA damage tolerance and resulting mutagenesis. The luminescence-based assays we developed allow for the quantitative determination of the degree of formation of ubiquitin thioester conjugate intermediates with both E1 and E2 proteins, autoubiquitination of the E3 protein involved, and ubiquitination of the final substrate. Thus, all covalent adducts along the cascade can be individually probed. We tested previously identified inhibitors of this ubiquitination cascade, finding generally good correspondence between compound potency trends determined by more traditional low-throughput methods and the present high-throughput ones. Conclusions These approaches are readily adaptable to other E1, E2, and E3 systems, and their substrates in both ubiquitination and ubiquitin-like post-translational modification cascades.
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Affiliation(s)
- Gabriel Fenteany
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.
| | - Paras Gaur
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.,Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Gaurav Sharma
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.,Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Lajos Pintér
- Visal Plus Ltd., Temesvári krt. 62, Szeged, 6726, Hungary
| | - Ernő Kiss
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.
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10
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Janel-Bintz R, Kuhn L, Frit P, Chicher J, Wagner J, Haracska L, Hammann P, Cordonnier AM. Proteomic Analysis of DNA Synthesis on a Structured DNA Template in Human Cellular Extracts: Interplay Between NHEJ and Replication-Associated Proteins. Proteomics 2020; 20:e1900184. [PMID: 31999075 DOI: 10.1002/pmic.201900184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/19/2019] [Indexed: 01/01/2023]
Abstract
It is established that short inverted repeats trigger base substitution mutagenesis in human cells. However, how the replication machinery deals with structured DNA is unknown. It has been previously reported that in human cell-free extracts, DNA primer extension using a structured single-stranded template is transiently blocked at DNA hairpins. Here, the proteomic analysis of proteins bound to the DNA template is reported and evidence that the DNA-PK complex (DNA-PKcs and the Ku heterodimer) recognizes, and is activated by, structured single-stranded DNA is provided. Hijacking the DNA-PK complex by double-stranded oligonucleotides results in a large removal of the pausing sites and an elevated DNA extension efficiency. Conversely, DNA-PKcs inhibition results in its stabilization on the template, along with other proteins acting downstream in the Non-Homologous End-Joining (NHEJ) pathway, especially the XRCC4-DNA ligase 4 complex and the cofactor PAXX. Retention of NHEJ factors to the DNA in the absence of DNA-PKcs activity correlates with additional halts of primer extension, suggesting that these proteins hinder the progression of the DNA synthesis at these sites. Overall these results raise the possibility that, upon binding to hairpins formed onto ssDNA during fork progression, the DNA-PK complex interferes with replication fork dynamics in vivo.
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Affiliation(s)
- Régine Janel-Bintz
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, CNRS, Illkirch, 67412, France
| | - Lauriane Kuhn
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg - Esplanade, FR1589, 67084, Strasbourg, France
| | - Philippe Frit
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Johana Chicher
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg - Esplanade, FR1589, 67084, Strasbourg, France
| | - Jérôme Wagner
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, CNRS, Illkirch, 67412, France
| | - Lajos Haracska
- Institute of Genetics, Biological Research Center, HU-6726, Szeged, Hungary
| | - Philippe Hammann
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg - Esplanade, FR1589, 67084, Strasbourg, France
| | - Agnès M Cordonnier
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, CNRS, Illkirch, 67412, France
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11
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Peng M, Cong K, Panzarino NJ, Nayak S, Calvo J, Deng B, Zhu LJ, Morocz M, Hegedus L, Haracska L, Cantor SB. Opposing Roles of FANCJ and HLTF Protect Forks and Restrain Replication during Stress. Cell Rep 2018; 24:3251-3261. [PMID: 30232006 PMCID: PMC6218949 DOI: 10.1016/j.celrep.2018.08.065] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/23/2018] [Accepted: 08/22/2018] [Indexed: 02/07/2023] Open
Abstract
The DNA helicase FANCJ is mutated in hereditary breast and ovarian cancer and Fanconi anemia (FA). Nevertheless, how loss of FANCJ translates to disease pathogenesis remains unclear. We addressed this question by analyzing proteins associated with replication forks in cells with or without FANCJ. We demonstrate that FANCJ-knockout (FANCJ-KO) cells have alterations in the replisome that are consistent with enhanced replication stress, including an aberrant accumulation of the fork remodeling factor helicase-like transcription factor (HLTF). Correspondingly, HLTF contributes to fork degradation in FANCJ-KO cells. Unexpectedly, the unrestrained DNA synthesis that characterizes HLTF-deficient cells is FANCJ dependent and correlates with S1 nuclease sensitivity and fork degradation. These results suggest that FANCJ and HLTF promote replication fork integrity, in part by counteracting each other to keep fork remodeling and elongation in check. Indicating one protein compensates for loss of the other, loss of both HLTF and FANCJ causes a more severe replication stress response.
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Affiliation(s)
- Min Peng
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ke Cong
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas J Panzarino
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sumeet Nayak
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jennifer Calvo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bin Deng
- Department of Biology/VGN Proteomics Facility, University of Vermont, Burlington, VT 05405, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Monika Morocz
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Lili Hegedus
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Lajos Haracska
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Sharon B Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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12
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Enyedi MZ, Jaksa G, Pintér L, Sükösd F, Gyuris Z, Hajdu A, Határvölgyi E, Priskin K, Haracska L. Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples. Oncotarget 2018; 7:61845-61859. [PMID: 27533253 PMCID: PMC5308695 DOI: 10.18632/oncotarget.11259] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples.
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Affiliation(s)
- Márton Zsolt Enyedi
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | | | | | - Farkas Sükösd
- Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | - Adrienn Hajdu
- Delta Bio 2000 Ltd., Szeged 6726, Hungary.,Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | | | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
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13
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Brasko C, Smith K, Molnar C, Farago N, Hegedus L, Balind A, Balassa T, Szkalisity A, Sukosd F, Kocsis K, Balint B, Paavolainen L, Enyedi MZ, Nagy I, Puskas LG, Haracska L, Tamas G, Horvath P. Intelligent image-based in situ single-cell isolation. Nat Commun 2018; 9:226. [PMID: 29335532 PMCID: PMC5768687 DOI: 10.1038/s41467-017-02628-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 12/14/2017] [Indexed: 01/18/2023] Open
Abstract
Quantifying heterogeneities within cell populations is important for many fields including cancer research and neurobiology; however, techniques to isolate individual cells are limited. Here, we describe a high-throughput, non-disruptive, and cost-effective isolation method that is capable of capturing individually targeted cells using widely available techniques. Using high-resolution microscopy, laser microcapture microscopy, image analysis, and machine learning, our technology enables scalable molecular genetic analysis of single cells, targetable by morphology or location within the sample. The isolation of single cells while retaining context is important for quantifying cellular heterogeneity but technically challenging. Here, the authors develop a high-throughput, scalable workflow for microscopy-based single cell isolation using machine-learning, high-throughput microscopy and laser capture microdissection.
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Affiliation(s)
- Csilla Brasko
- University of Szeged, Szeged, Hungary Közép fasor 52, 6726, Szeged, Hungary
| | - Kevin Smith
- School of Computer Science and Communication, KTH Royal Institute of Technology, Lindstedtsvägen 3-5, 10044, Stockholm, Sweden.,Science for Life Laboratory, Tomtebodavägen 23A, 17121, Solna, Sweden
| | - Csaba Molnar
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary
| | - Nora Farago
- University of Szeged, Szeged, Hungary Közép fasor 52, 6726, Szeged, Hungary.,Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary.,Avidin Biotechnology Ltd, Alsó Kikötő sor 11, 6726, Szeged, Hungary
| | - Lili Hegedus
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary
| | - Arpad Balind
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary
| | - Tamas Balassa
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary
| | - Abel Szkalisity
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary
| | - Farkas Sukosd
- University of Szeged, Szeged, Hungary Közép fasor 52, 6726, Szeged, Hungary
| | - Katalin Kocsis
- University of Szeged, Szeged, Hungary Közép fasor 52, 6726, Szeged, Hungary
| | - Balazs Balint
- SeqOmics Biotechnology Ltd, Vállalkozók útja 7, 6782, Mórahalom, Hungary
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, Helsinki, 00014, Finland
| | - Marton Z Enyedi
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary
| | - Istvan Nagy
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary.,SeqOmics Biotechnology Ltd, Vállalkozók útja 7, 6782, Mórahalom, Hungary
| | - Laszlo G Puskas
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary.,Avidin Biotechnology Ltd, Alsó Kikötő sor 11, 6726, Szeged, Hungary
| | - Lajos Haracska
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary
| | - Gabor Tamas
- University of Szeged, Szeged, Hungary Közép fasor 52, 6726, Szeged, Hungary
| | - Peter Horvath
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., 6726, Szeged, Hungary. .,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, Helsinki, 00014, Finland.
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14
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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: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Kriston-Pál É, Czibula Á, Gyuris Z, Balka G, Seregi A, Sükösd F, Süth M, Kiss-Tóth E, Haracska L, Uher F, Monostori É. Characterization and therapeutic application of canine adipose mesenchymal stem cells to treat elbow osteoarthritis. Can J Vet Res 2017; 81:73-78. [PMID: 28197017 PMCID: PMC5220603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/19/2016] [Indexed: 06/06/2023]
Abstract
Visceral adipose tissue (AT) obtained from surgical waste during routine ovariectomies was used as a source for isolating canine mesenchymal stem cells (MSCs). As determined by cytofluorimetry, passage 2 cells expressed MSC markers CD44 and CD90 and were negative for lineage-specific markers CD34 and CD45. The cells differentiated toward osteogenic, adipogenic, and chondrogenic directions. With therapeutic aims, 30 dogs (39 joints) suffering from elbow dysplasia (ED) and osteoarthritis (OA) were intra-articularly transplanted with allogeneic MSCs suspended in 0.5% hyaluronic acid (HA). A highly significant improvement was achieved without any medication as demonstrated by the degree of lameness during the follow-up period of 1 y. Control arthroscopy of 1 transplanted dog indicated that the cartilage had regenerated. Histological analysis of the cartilage biopsy confirmed that the regenerated cartilage was of hyaline type. These results demonstrate that transplantation of allogeneic adipose tissue-derived mesenchymal stem cells (AT-MSCs) is a novel, noninvasive, and highly effective therapeutic tool in treating canine elbow dysplasia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Éva Monostori
- Address all correspondence to Dr. Éva Monostori; telephone: +36-62-599-600; fax: +36-62-433-503; e-mail:
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16
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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: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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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: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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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: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Baldeck N, Janel-Bintz R, Wagner J, Tissier A, Fuchs RP, Burkovics P, Haracska L, Despras E, Bichara M, Chatton B, Cordonnier AM. FF483-484 motif of human Polη mediates its interaction with the POLD2 subunit of Polδ and contributes to DNA damage tolerance. Nucleic Acids Res 2015; 43:2116-25. [PMID: 25662213 PMCID: PMC4344513 DOI: 10.1093/nar/gkv076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Switching between replicative and translesion synthesis (TLS) DNA polymerases are crucial events for the completion of genomic DNA synthesis when the replication machinery encounters lesions in the DNA template. In eukaryotes, the translesional DNA polymerase η (Polη) plays a central role for accurate bypass of cyclobutane pyrimidine dimers, the predominant DNA lesions induced by ultraviolet irradiation. Polη deficiency is responsible for a variant form of the Xeroderma pigmentosum (XPV) syndrome, characterized by a predisposition to skin cancer. Here, we show that the FF483-484 amino acids in the human Polη (designated F1 motif) are necessary for the interaction of this TLS polymerase with POLD2, the B subunit of the replicative DNA polymerase δ, both in vitro and in vivo. Mutating this motif impairs Polη function in the bypass of both an N-2-acetylaminofluorene adduct and a TT-CPD lesion in cellular extracts. By complementing XPV cells with different forms of Polη, we show that the F1 motif contributes to the progression of DNA synthesis and to the cell survival after UV irradiation. We propose that the integrity of the F1 motif of Polη, necessary for the Polη/POLD2 interaction, is required for the establishment of an efficient TLS complex.
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Affiliation(s)
- Nadège Baldeck
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, Illkirch 67412, France
| | - Régine Janel-Bintz
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, Illkirch 67412, France
| | - Jérome Wagner
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, Illkirch 67412, France
| | - Agnès Tissier
- UMR-S1052, Inserm, Centre de Recherche en Cancérologie de Lyon, Lyon 69000, France
| | - Robert P Fuchs
- Cancer Research Center of Marseille (CRCM), Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7258, Marseille 13009, France
| | - Peter Burkovics
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, HU-6726 Szeged, Hungary
| | - Lajos Haracska
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, HU-6726 Szeged, Hungary
| | - Emmanuelle Despras
- Université Paris-Sud, CNRS-UMR8200, Equipe labellisée Ligue Contre le Cancer, Gustave Roussy, Villejuif, France
| | - Marc Bichara
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, Illkirch 67412, France
| | - Bruno Chatton
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, Illkirch 67412, France
| | - Agnès M Cordonnier
- Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR7242, Illkirch 67412, France
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20
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Daraba A, Gali VK, Halmai M, Haracska L, Unk I. Def1 promotes the degradation of Pol3 for polymerase exchange to occur during DNA-damage--induced mutagenesis in Saccharomyces cerevisiae. PLoS Biol 2014; 12:e1001771. [PMID: 24465179 PMCID: PMC3897375 DOI: 10.1371/journal.pbio.1001771] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/09/2013] [Indexed: 01/19/2023] Open
Abstract
DNA damages hinder the advance of replication forks because of the inability of the replicative polymerases to synthesize across most DNA lesions. Because stalled replication forks are prone to undergo DNA breakage and recombination that can lead to chromosomal rearrangements and cell death, cells possess different mechanisms to ensure the continuity of replication on damaged templates. Specialized, translesion synthesis (TLS) polymerases can take over synthesis at DNA damage sites. TLS polymerases synthesize DNA with a high error rate and are responsible for damage-induced mutagenesis, so their activity must be strictly regulated. However, the mechanism that allows their replacement of the replicative polymerase is unknown. Here, using protein complex purification and yeast genetic tools, we identify Def1 as a key factor for damage-induced mutagenesis in yeast. In in vivo experiments we demonstrate that upon DNA damage, Def1 promotes the ubiquitylation and subsequent proteasomal degradation of Pol3, the catalytic subunit of the replicative polymerase δ, whereas Pol31 and Pol32, the other two subunits of polymerase δ, are not affected. We also show that purified Pol31 and Pol32 can form a complex with the TLS polymerase Rev1. Our results imply that TLS polymerases carry out DNA lesion bypass only after the Def1-assisted removal of Pol3 from the stalled replication fork.
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Affiliation(s)
- Andreea Daraba
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Vamsi K. Gali
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Miklós Halmai
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lajos Haracska
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ildiko Unk
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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21
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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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22
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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: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Csoboz B, Balogh GE, Kusz E, Gombos I, Peter M, Crul T, Gungor B, Haracska L, Bogdanovics G, Torok Z, Horvath I, Vigh L. Membrane fluidity matters: Hyperthermia from the aspects of lipids and membranes. Int J Hyperthermia 2013; 29:491-9. [DOI: 10.3109/02656736.2013.808765] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Sebesta M, Burkovics P, Juhasz S, Zhang S, Szabo JE, Lee MYWT, Haracska L, Krejci L. Role of PCNA and TLS polymerases in D-loop extension during homologous recombination in humans. DNA Repair (Amst) 2013; 12:691-8. [PMID: 23731732 PMCID: PMC3744802 DOI: 10.1016/j.dnarep.2013.05.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 04/29/2013] [Accepted: 05/02/2013] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is essential for maintaining genomic integrity, which is challenged by a wide variety of potentially lethal DNA lesions. Regardless of the damage type, recombination is known to proceed by RAD51-mediated D-loop formation, followed by DNA repair synthesis. Nevertheless, the participating polymerases and extension mechanism are not well characterized. Here, we present a reconstitution of this step using purified human proteins. In addition to Pol δ, TLS polymerases, including Pol η and Pol κ, also can extend D-loops. In vivo characterization reveals that Pol η and Pol κ are involved in redundant pathways for HR. In addition, the presence of PCNA on the D-loop regulates the length of the extension tracks by recruiting various polymerases and might present a regulatory point for the various recombination outcomes.
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Affiliation(s)
- Marek Sebesta
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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25
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Ferencz C, Petrovszki P, Kóta Z, Fodor-Ayaydin E, Haracska L, Bóta A, Varga Z, Dér A, Marsh D, Páli T. Estimating the rotation rate in the vacuolar proton-ATPase in native yeast vacuolar membranes. Eur Biophys J 2012; 42:147-58. [PMID: 23160754 DOI: 10.1007/s00249-012-0871-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/10/2012] [Accepted: 10/25/2012] [Indexed: 11/25/2022]
Abstract
The rate of rotation of the rotor in the yeast vacuolar proton-ATPase (V-ATPase), relative to the stator or steady parts of the enzyme, is estimated in native vacuolar membrane vesicles from Saccharomyces cerevisiae under standardised conditions. Membrane vesicles are formed spontaneously after exposing purified yeast vacuoles to osmotic shock. The fraction of total ATPase activity originating from the V-ATPase is determined by using the potent and specific inhibitor of the enzyme, concanamycin A. Inorganic phosphate liberated from ATP in the vacuolar membrane vesicle system, during ten min of ATPase activity at 20 °C, is assayed spectrophotometrically for different concanamycin A concentrations. A fit of the quadratic binding equation, assuming a single concanamycin A binding site on a monomeric V-ATPase (our data are incompatible with models assuming multiple binding sites), to the inhibitor titration curve determines the concentration of the enzyme. Combining this with the known ATP/rotation stoichiometry of the V-ATPase and the assayed concentration of inorganic phosphate liberated by the V-ATPase, leads to an average rate of ~10 Hz for full 360° rotation (and a range of 6-32 Hz, considering the ± standard deviation of the enzyme concentration), which, from the time-dependence of the activity, extrapolates to ~14 Hz (8-48 Hz) at the beginning of the reaction. These are lower-limit estimates. To our knowledge, this is the first report of the rotation rate in a V-ATPase that is not subjected to genetic or chemical modification and is not fixed to a solid support; instead it is functioning in its native membrane environment.
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Affiliation(s)
- Csilla Ferencz
- Institute of Biophysics, Biological Research Centre, Temesvári krt. 62, 6726, Szeged, Hungary
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26
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Juhasz S, Balogh D, Hajdu I, Burkovics P, Villamil MA, Zhuang Z, Haracska L. Characterization of human Spartan/C1orf124, an ubiquitin-PCNA interacting regulator of DNA damage tolerance. Nucleic Acids Res 2012; 40:10795-808. [PMID: 22987070 PMCID: PMC3510514 DOI: 10.1093/nar/gks850] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Unrepaired DNA damage may arrest ongoing replication forks, potentially resulting in fork
collapse, increased mutagenesis and genomic instability. Replication through DNA lesions
depends on mono- and polyubiquitylation of proliferating cell nuclear antigen (PCNA),
which enable translesion synthesis (TLS) and template switching, respectively. A proper
replication fork rescue is ensured by the dynamic ubiquitylation and deubiquitylation of
PCNA; however, as yet, little is known about its regulation. Here, we show that human
Spartan/C1orf124 protein provides a higher cellular level of ubiquitylated-PCNA by which
it regulates the choice of DNA damage tolerance pathways. We find that Spartan is
recruited to sites of replication stress, a process that depends on its PCNA- and
ubiquitin-interacting domains and the RAD18 PCNA ubiquitin ligase. Preferential
association of Spartan with ubiquitin-modified PCNA protects against PCNA deubiquitylation
by ubiquitin-specific protease 1 and facilitates the access of a TLS polymerase to the
replication fork. In concert, depletion of Spartan leads to increased sensitivity to DNA
damaging agents and causes elevated levels of sister chromatid exchanges. We propose that
Spartan promotes genomic stability by regulating the choice of rescue of stalled
replication fork, whose mechanism includes its interaction with ubiquitin-conjugated PCNA
and protection against PCNA deubiquitylation.
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Affiliation(s)
- Szilvia Juhasz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged 6726, Hungary
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27
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Ciccia A, Nimonkar AV, Hu Y, Hajdu I, Achar YJ, Izhar L, Petit SA, Adamson B, Yoon JC, Kowalczykowski SC, Livingston DM, Haracska L, Elledge SJ. Polyubiquitinated PCNA recruits the ZRANB3 translocase to maintain genomic integrity after replication stress. Mol Cell 2012; 47:396-409. [PMID: 22704558 DOI: 10.1016/j.molcel.2012.05.024] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/12/2012] [Accepted: 05/17/2012] [Indexed: 10/28/2022]
Abstract
Completion of DNA replication after replication stress depends on PCNA, which undergoes monoubiquitination to stimulate direct bypass of DNA lesions by specialized DNA polymerases or is polyubiquitinated to promote recombination-dependent DNA synthesis across DNA lesions by template switching mechanisms. Here we report that the ZRANB3 translocase, a SNF2 family member related to the SIOD disorder SMARCAL1 protein, is recruited by polyubiquitinated PCNA to promote fork restart following replication arrest. ZRANB3 depletion in mammalian cells results in an increased frequency of sister chromatid exchange and DNA damage sensitivity after treatment with agents that cause replication stress. Using in vitro biochemical assays, we show that recombinant ZRANB3 remodels DNA structures mimicking stalled replication forks and disassembles recombination intermediates. We therefore propose that ZRANB3 maintains genomic stability at stalled or collapsed replication forks by facilitating fork restart and limiting inappropriate recombination that could occur during template switching events.
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Affiliation(s)
- Alberto Ciccia
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA
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28
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Janel-Bintz R, Wagner J, Haracska L, Mah-Becherel MCM, Bichara M, Fuchs RP, Cordonnier AM. Evidence for a Rad18-independent frameshift mutagenesis pathway in human cell-free extracts. PLoS One 2012; 7:e36004. [PMID: 22558303 PMCID: PMC3338768 DOI: 10.1371/journal.pone.0036004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 03/29/2012] [Indexed: 12/19/2022] Open
Abstract
Bypass of replication blocks by specialized DNA polymerases is crucial for cell survival but may promote mutagenesis and genome instability. To gain insight into mutagenic sub-pathways that coexist in mammalian cells, we examined N-2-acetylaminofluorene (AAF)-induced frameshift mutagenesis by means of SV40-based shuttle vectors containing a single adduct. We found that in mammalian cells, as previously observed in E. coli, modification of the third guanine of two target sequences, 5'-GGG-3' (3G) and 5'-GGCGCC-3' (NarI site), induces –1 and –2 frameshift mutations, respectively. Using an in vitro assay for translesion synthesis, we investigated the biochemical control of these events. We showed that Pol eta, but neither Pol iota nor Pol zeta, plays a major role in the frameshift bypass of the AAF adduct located in the 3G sequence. By complementing PCNA-depleted extracts with either a wild-type or a non-ubiquitinatable form of PCNA, we found that this Pol eta-mediated pathway requires Rad18 and ubiquitination of PCNA. In contrast, when the AAF adduct is located within the NarI site, TLS is only partially dependent upon Pol eta and Rad18, unravelling the existence of alternative pathways that concurrently bypass this lesion.
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Affiliation(s)
- Régine Janel-Bintz
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Jérôme Wagner
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Marcia Chia Miao Mah-Becherel
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Marc Bichara
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Robert P. Fuchs
- Campus J. Aiguier, UPR3081 Genome Instability and Carcinogenesis, Marseille, France
| | - Agnès M. Cordonnier
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
- * E-mail:
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29
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Gali H, Juhasz S, Morocz M, Hajdu I, Fatyol K, Szukacsov V, Burkovics P, Haracska L. Role of SUMO modification of human PCNA at stalled replication fork. Nucleic Acids Res 2012; 40:6049-59. [PMID: 22457066 PMCID: PMC3401441 DOI: 10.1093/nar/gks256] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) can be generated not only by reactive agents but also as a result of replication fork collapse at unrepaired DNA lesions. Whereas ubiquitylation of proliferating cell nuclear antigen (PCNA) facilitates damage bypass, modification of yeast PCNA by small ubiquitin-like modifier (SUMO) controls recombination by providing access for the Srs2 helicase to disrupt Rad51 nucleoprotein filaments. However, in human cells, the roles of PCNA SUMOylation have not been explored. Here, we characterize the modification of human PCNA by SUMO in vivo as well as in vitro. We establish that human PCNA can be SUMOylated at multiple sites including its highly conserved K164 residue and that SUMO modification is facilitated by replication factor C (RFC). We also show that expression of SUMOylation site PCNA mutants leads to increased DSB formation in the Rad18−/− cell line where the effect of Rad18-dependent K164 PCNA ubiquitylation can be ruled out. Moreover, expression of PCNA-SUMO1 fusion prevents DSB formation as well as inhibits recombination if replication stalls at DNA lesions. These findings suggest the importance of SUMO modification of human PCNA in preventing replication fork collapse to DSB and providing genome stability.
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Affiliation(s)
- Himabindu Gali
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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30
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Sebesta M, Burkovics P, Haracska L, Krejci L. Reconstitution of DNA repair synthesis in vitro and the role of polymerase and helicase activities. DNA Repair (Amst) 2011; 10:567-76. [PMID: 21565563 PMCID: PMC3119790 DOI: 10.1016/j.dnarep.2011.03.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 03/04/2011] [Accepted: 03/08/2011] [Indexed: 12/15/2022]
Abstract
The error-free repair of double-strand DNA breaks by homologous recombination (HR) ensures genomic stability using undamaged homologous sequence to copy genetic information. While some of the aspects of the initial steps of HR are understood, the molecular mechanisms underlying events downstream of the D-loop formation remain unclear. Therefore, we have reconstituted D-loop-based in vitro recombination-associated DNA repair synthesis assay and tested the efficacy of polymerases Pol δ and Pol η to extend invaded primer, and the ability of three helicases (Mph1, Srs2 and Sgs1) to displace this extended primer. Both Pol δ and Pol η extended up to 50% of the D-loop substrate, but differed in product length and dependency on proliferating cell nuclear antigen (PCNA). Mph1, but not Srs2 or Sgs1, displaced the extended primer very efficiently, supporting putative role of Mph1 in promoting the synthesis-dependent strand-annealing pathway. The experimental system described here can be employed to increase our understanding of HR events following D-loop formation, as well as the regulatory mechanisms involved.
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Affiliation(s)
- Marek Sebesta
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, Czech Republic
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31
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Ai Y, Wang J, Johnson RE, Haracska L, Prakash L, Zhuang Z. A novel ubiquitin binding mode in the S. cerevisiae translesion synthesis DNA polymerase η. Mol Biosyst 2011; 7:1874-82. [PMID: 21483899 DOI: 10.1039/c0mb00355g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ubiquitin binding zinc finger (UBZ) domain in the C-terminal portion of Polη has been found to interact with ubiquitin. However, the affinity between the Polη UBZ and ubiquitin was shown to be low with a previously reported K(d) of 73-81 μM. This low-affinity binding between Polη UBZ and ubiquitin has been difficult to reconcile with its presumed role in translesion synthesis as suggested by genetic and cell biology studies. In this work, we constructed a minimal S. cerevisiae Polη UBZ domain and probed the Polη UBZ-ubiquitin interaction using a surface plasmon resonance (SPR) technique. Our quantitative binding data between the wild-type or mutant Polη UBZ and ubiquitin revealed an interesting divergence between the Polη UBZ from S. cerevisiae and humans. Moreover, we found that the C-terminal portion of yeast Polη (amino acid 515-632) binds ubiquitin with a much higher affinity than the minimal UBZ domain. Further, distinct ubiquitin-binding kinetics were observed for the C-terminal portion of Polη and the isolated UBZ domain. This observation raised the interesting possibility that the Polη C-terminal portion binds ubiquitin in a novel mode that affords higher affinity. Our findings have broader implication in understanding the generally weak interaction between the known ubiquitin-binding domains and ubiquitin.
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Affiliation(s)
- Yongxing Ai
- Department of Chemistry and Biochemistry, 214A Drake Hall, University of Delaware, Newark, DE 19716, USA
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32
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Chen J, Ai Y, Wang J, Haracska L, Zhuang Z. Chemically ubiquitylated PCNA as a probe for eukaryotic translesion DNA synthesis. Nat Chem Biol 2010; 6:270-2. [DOI: 10.1038/nchembio.316] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 12/04/2009] [Indexed: 01/24/2023]
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Jansen JG, Tsaalbi-Shtylik A, Hendriks G, Verspuy J, Gali H, Haracska L, de Wind N. Mammalian polymerase zeta is essential for post-replication repair of UV-induced DNA lesions. DNA Repair (Amst) 2009; 8:1444-51. [PMID: 19783229 DOI: 10.1016/j.dnarep.2009.09.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 08/17/2009] [Accepted: 09/10/2009] [Indexed: 01/11/2023]
Abstract
DNA polymerase zeta is believed to be an essential constituent of DNA damage tolerance, comprising several pathways that allow the replication of DNA templates containing unrepaired damage. We wanted to better define the role of polymerase zeta in DNA damage tolerance in mammalian cells. To this aim we have investigated replication of ultraviolet light-damaged DNA templates in mouse embryonic fibroblasts deficient for Rev3, the catalytic subunit of polymerase zeta. We found that Rev3 is important for a post-replication repair pathway of helix-distorting [6-4]pyrimidine-pyrimidone photoproducts and, to a lesser extent, of cyclobutane pyrimidine dimers. Unlike its partner Rev1, Rev3 appears not to be involved in an immediate translesion synthesis pathway at a stalled replication fork. The deficiency of Rev3(-/-) MEFs in post-replication repair of different photoproducts contributes to the extreme sensitivity of these cells to UV light.
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Affiliation(s)
- Jacob G Jansen
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, PO Box 9600, 2300 RC Leiden, The Netherlands
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Burkovics P, Hajdú I, Szukacsov V, Unk I, Haracska L. Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'-5' exonuclease activities of human Ape2 in repair of oxidative DNA damage. Nucleic Acids Res 2009; 37:4247-55. [PMID: 19443450 PMCID: PMC2715233 DOI: 10.1093/nar/gkp357] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human Ape2 protein has 3' phosphodiesterase activity for processing 3'-damaged DNA termini, 3'-5' exonuclease activity that supports removal of mismatched nucleotides from the 3'-end of DNA, and a somewhat weak AP-endonuclease activity. However, very little is known about the role of Ape2 in DNA repair processes. Here, we examine the effect of interaction of Ape2 with proliferating cell nuclear antigen (PCNA) on its enzymatic activities and on targeting Ape2 to oxidative DNA lesions. We show that PCNA strongly stimulates the 3'-5' exonuclease and 3' phosphodiesterase activities of Ape2, but has no effect on its AP-endonuclease activity. Moreover, we find that upon hydrogen-peroxide treatment Ape2 redistributes to nuclear foci where it colocalizes with PCNA. In concert with these results, we provide biochemical evidence that Ape2 can reduce the mutagenic consequences of attack by reactive oxygen species not only by repairing 3'-damaged termini but also by removing 3'-end adenine opposite from 8-oxoG. Based on these findings we suggest the involvement of Ape2 in repair of oxidative DNA damage and PCNA-dependent repair synthesis.
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Affiliation(s)
- Peter Burkovics
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged H-6701, Hungary
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35
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Abstract
In Saccharomyces cerevisiae, Rev1 functions in translesion DNA synthesis (TLS) together with polymerase zeta (Pol zeta), comprised of the Rev3 catalytic and Rev7 accessory subunits. Rev1 plays an indispensable structural role in promoting Pol zeta function, and deletion of the Rev1-C terminal region that is involved in physical interactions with Rev3 inactivates Pol zeta function in TLS. In humans, however, Rev1 has been shown to physically interact with the Y-family polymerases Pol eta, Pol iota, and Pol kappa, and the Rev1 C terminus mediates these interactions. Since all the available genetic and biochemical evidence in yeast support the requirement of Rev1 as a structural element for Pol zeta and not for Pol eta, these observations have raised the possibility that in its structural role, Rev1 has diverged between yeast and humans. Here we show that although in yeast a stable Rev1-Pol eta complex can be formed, this complex formation involves the polymerase-associated domain of Rev1 and not the Rev1 C terminus as in humans. We also found that the DNA synthesis activity of Rev1 is enhanced in this complex. We discuss the implications of these and other observations for the possible divergence of Rev1's structural role between yeast and humans.
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Affiliation(s)
- Narottam Acharya
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555-1061, USA
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Acharya N, Brahma A, Haracska L, Prakash L, Prakash S. Mutations in the ubiquitin binding UBZ motif of DNA polymerase eta do not impair its function in translesion synthesis during replication. Mol Cell Biol 2007; 27:7266-72. [PMID: 17709386 PMCID: PMC2168893 DOI: 10.1128/mcb.01196-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Treatment of Saccharomyces cerevisiae cells with DNA-damaging agents elicits lysine 164-linked PCNA monoubiquitination by Rad6-Rad18. Recently, a number of ubiquitin (Ub) binding domains (UBDs) have been identified in translesion synthesis (TLS) DNA polymerases and it has been proposed that the UBD in a TLS polymerase affects its binding to Ub on PCNA and that this binding mode is indispensable for a TLS polymerase to access PCNA at the site of a stalled replication fork. To evaluate the contribution of the binding of UBDs to the Ub moiety on PCNA in TLS, we have examined the effects of mutations in the C2H2 zinc binding motif and in the conserved D570 residue that lies in the alpha-helix portion of the UBZ domain of yeast Poleta. We find that mutations in the C2H2 motif have no perceptible effect on UV sensitivity or UV mutagenesis, whereas a mutation of the D570 residue adversely affects Poleta function. The stimulation of DNA synthesis by Poleta with PCNA or Ub-PCNA was not affected by mutations in the C2H2 motif or the D570 residue. These observations lead us to suggest that the binding of Ub on PCNA via its UBZ domain is not a necessary requirement for the ability of polymerase eta to function in TLS during replication.
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Affiliation(s)
- Narottam Acharya
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 6.104 Blocker Medical Research Building, 301 University Blvd., Galveston, TX 77555-1061, USA
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37
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Unk I, Hajdú I, Fátyol K, Szakál B, Blastyák A, Bermudez V, Hurwitz J, Prakash L, Prakash S, Haracska L. Human SHPRH is a ubiquitin ligase for Mms2-Ubc13-dependent polyubiquitylation of proliferating cell nuclear antigen. Proc Natl Acad Sci U S A 2006; 103:18107-12. [PMID: 17108083 PMCID: PMC1838714 DOI: 10.1073/pnas.0608595103] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human SHPRH gene is located at the 6q24 chromosomal region, and loss of heterozygosity in this region is seen in a wide variety of cancers. SHPRH is a member of the SWI/SNF family of ATPases/helicases, and it possesses a C(3)HC(4) RING motif characteristic of ubiquitin ligase proteins. In both of these features, SHPRH resembles the yeast Rad5 protein, which, together with Mms2-Ubc13, promotes replication through DNA lesions via an error-free postreplicational repair pathway. Genetic evidence in yeast has indicated a role for Rad5 as a ubiquitin ligase in mediating the Mms2-Ubc13-dependent polyubiquitylation of proliferating cell nuclear antigen. Here we show that SHPRH is a functional homolog of Rad5. Similar to Rad5, SHPRH physically interacts with the Rad6-Rad18 and Mms2-Ubc13 complexes, and we show that SHPRH protein is a ubiquitin ligase indispensable for Mms2-Ubc13-dependent polyubiquitylation of proliferating cell nuclear antigen. Based on these observations, we predict a role for SHPRH in promoting error-free replication through DNA lesions. Such a role for SHPRH is consistent with the observation that this gene is mutated in a number of cancer cell lines, including those from melanomas and ovarian cancers, which raises the strong possibility that SHPRH function is an important deterrent to mutagenesis and carcinogenesis in humans.
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Affiliation(s)
- Ildiko Unk
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Ildikó Hajdú
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Károly Fátyol
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Barnabás Szakál
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - András Blastyák
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Vladimir Bermudez
- Molecular Biology Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10021; and
| | - Jerard Hurwitz
- Molecular Biology Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10021; and
- To whom correspondence should be addressed. E-mail:
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Lajos Haracska
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
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Johnson RE, Haracska L, Prakash L, Prakash S. Role of hoogsteen edge hydrogen bonding at template purines in nucleotide incorporation by human DNA polymerase iota. Mol Cell Biol 2006; 26:6435-41. [PMID: 16914729 PMCID: PMC1592827 DOI: 10.1128/mcb.00851-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human DNA polymerase iota (Pol iota) differs from other DNA polymerases in that it exhibits a marked template specificity, being more efficient and accurate opposite template purines than opposite pyrimidines. The crystal structures of Pol iota with template A and incoming dTTP and with template G and incoming dCTP have revealed that in the Pol iota active site, the templating purine adopts a syn conformation and forms a Hoogsteen base pair with the incoming pyrimidine which remains in the anti conformation. By using 2-aminopurine and purine as the templating residues, which retain the normal N7 position but lack the N(6) of an A or the O(6) of a G, here we provide evidence that whereas hydrogen bonding at N(6) is dispensable for the proficient incorporation of a T opposite template A, hydrogen bonding at O(6) is a prerequisite for C incorporation opposite template G. To further analyze the contributions of O(6) and N7 hydrogen bonding to DNA synthesis by Pol iota, we have examined its proficiency for replicating through the (6)O-methyl guanine and 8-oxoguanine lesions, which affect the O(6) and N7 positions of template G, respectively. We conclude from these studies that for proficient T incorporation opposite template A, only the N7 hydrogen bonding is required, but for proficient C incorporation opposite template G, hydrogen bonding at both the N7 and O(6) is an imperative. The dispensability of N(6) hydrogen bonding for proficient T incorporation opposite template A has important biological implications, as that would endow Pol iota with the ability to replicate through lesions which impair the Watson-Crick hydrogen bonding potential at both the N1 and N(6) positions of templating A.
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Affiliation(s)
- Robert E Johnson
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, 6.104 Blocker Medical Research Building, 11th and Mechanic Streets, Galveston, TX 77555-1061, USA
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Gangavarapu V, Haracska L, Unk I, Johnson RE, Prakash S, Prakash L. Mms2-Ubc13-dependent and -independent roles of Rad5 ubiquitin ligase in postreplication repair and translesion DNA synthesis in Saccharomyces cerevisiae. Mol Cell Biol 2006; 26:7783-90. [PMID: 16908531 PMCID: PMC1636848 DOI: 10.1128/mcb.01260-06] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Rad6-Rad18 ubiquitin-conjugating enzyme complex of Saccharomyces cerevisiae promotes replication through DNA lesions via three separate pathways that include translesion synthesis (TLS) by DNA polymerases eta and zeta and postreplicational repair (PRR) of discontinuities that form in the newly synthesized DNA opposite from DNA lesions, mediated by the Mms2-Ubc13 ubiquitin-conjugating enzyme and Rad5. Rad5 is an SWI/SNF family ATPase, and additionally, it functions as a ubiquitin ligase in the ubiquitin conjugation reaction. To decipher the roles of these Rad5 activities in lesion bypass, here we examine the effects of mutations in the Rad5 ATPase and ubiquitin ligase domains on the PRR of UV-damaged DNA and on UV-induced mutagenesis. Even though the ATPase-defective mutation confers only a modest degree of UV sensitivity whereas the ubiquitin ligase mutation causes a high degree of UV sensitivity, we find that both of these mutations produce the same high level of PRR defect as that conferred by the highly UV-sensitive rad5Delta mutation. From these studies, we infer a requirement of the Rad5 ATPase and ubiquitin ligase activities in PRR, and based upon the effects of different rad5 mutations on UV mutagenesis, we suggest a role for Rad5 in affecting the efficiency of lesion bypass by the TLS polymerases. In contrast to the role of Rad5 in PRR, however, where its function is coupled with that of Mms2-Ubc13, Rad5 function in TLS would be largely independent of this ubiquitin-conjugating enzyme complex.
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Affiliation(s)
- Venkateswarlu Gangavarapu
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, Galveston, TX 77555-1061.
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40
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Burkovics P, Szukacsov V, Unk I, Haracska L. Human Ape2 protein has a 3'-5' exonuclease activity that acts preferentially on mismatched base pairs. Nucleic Acids Res 2006; 34:2508-15. [PMID: 16687656 PMCID: PMC1459411 DOI: 10.1093/nar/gkl259] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA damage, such as abasic sites and DNA strand breaks with 3′-phosphate and 3′-phosphoglycolate termini present cytotoxic and mutagenic threats to the cell. Class II AP endonucleases play a major role in the repair of abasic sites as well as of 3′-modified termini. Human cells contain two class II AP endonucleases, the Ape1 and Ape2 proteins. Ape1 possesses a strong AP-endonuclease activity and weak 3′-phosphodiesterase and 3′–5′ exonuclease activities, and it is considered to be the major AP endonuclease in human cells. Much less is known about Ape2, but its importance is emphasized by the growth retardation and dyshematopoiesis accompanied by G2/M arrest phenotype of the APE2-null mice. Here, we describe the biochemical characteristics of human Ape2. We find that Ape2 exhibits strong 3′–5′ exonuclease and 3′-phosphodiesterase activities and has only a very weak AP-endonuclease activity. Mutation of the active-site residue Asp 277 to Ala in Ape2 inactivates all these activities. We also demonstrate that Ape2 preferentially acts at mismatched deoxyribonucleotides at the recessed 3′-termini of a partial DNA duplex. Based on these results we suggest a novel role for human Ape2 as a 3′–5′ exonuclease.
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Affiliation(s)
| | | | | | - Lajos Haracska
- To whom correspondence should be addressed. Tel: 36 62 599666; Fax: 36 62 433503;
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41
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Haracska L, Unk I, Prakash L, Prakash S. Ubiquitylation of yeast proliferating cell nuclear antigen and its implications for translesion DNA synthesis. Proc Natl Acad Sci U S A 2006; 103:6477-82. [PMID: 16611731 PMCID: PMC1458909 DOI: 10.1073/pnas.0510924103] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Rad6-Rad18 ubiquitin-conjugating enzyme complex promotes replication through DNA lesions by means of at least three different pathways: the DNA polymerase (Pol) eta- and zeta-dependent translesion DNA synthesis (TLS) and a Rad5-Mms2-Ubc13-dependent pathway. In DNA-damaged yeast cells proliferating cell nuclear antigen (PCNA) becomes monoubiquitylated at the K164 residue, and genetic studies in yeast have indicated a requirement for this modification in TLS mediated by Poleta and Polzeta. To be able to decipher the role of PCNA monoubiquitylation in the TLS process, we have reconstituted this PCNA modification in vitro from purified yeast proteins. We show that, in addition to the requirement for Rad6-Rad18, the reaction depends on the loading of the PCNA homotrimeric ring onto the DNA by replication factor C and that all three PCNA monomers become efficiently ubiquitylated. The availability of PCNA monoubiquitylated on all of its three monomers has enabled us to examine the effects of this PCNA modification on DNA synthesis by Pols delta, eta, zeta, and Rev1. Contrary to the prevailing ideas that presume a role for PCNA ubiquitylation in the disruption of Poldelta's binding to PCNA or in the enhancement of the binding affinity of the TLS Pols for PCNA, we find that PCNA ubiquitylation does not affect any of these processes. These observations lead us to suggest a role for PCNA monoubiquitylation in disrupting the PCNA binding of a protein(s) that otherwise is inhibitory to the binding of PCNA by TLS Pols.
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Affiliation(s)
- Lajos Haracska
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6701 Szeged, Hungary; and
| | - Ildiko Unk
- *Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6701 Szeged, Hungary; and
| | - Louise Prakash
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, TX 77555
| | - Satya Prakash
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, TX 77555
- To whom correspondence should be addressed. E-mail:
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42
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Acharya N, Haracska L, Johnson RE, Unk I, Prakash S, Prakash L. Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain. Mol Cell Biol 2005; 25:9734-40. [PMID: 16227619 PMCID: PMC1265840 DOI: 10.1128/mcb.25.21.9734-9740.2005] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Rev1 protein of Saccharomyces cerevisiae functions in translesion synthesis (TLS) together with DNA polymerase (Pol) zeta, which is comprised of the Rev3 catalytic and the Rev7 accessory subunits. Rev1, a member of the Y family of Pols, differs from other members in its high degree of specificity for incorporating a C opposite template G as well as opposite an abasic site. Although Rev1 is indispensable for Polzeta-dependent TLS, its DNA synthetic activity is not required for many of the Polzeta-dependent lesion bypass events. This observation has suggested a structural role for Rev1 in this process. Here we show that in yeast, Rev1 forms a stable complex with Rev7, and the two proteins copurify. Importantly, the polymerase-associated domain (PAD) of Rev1 mediates its binding to Rev7. These observations reveal a novel role for the PAD region of Rev1 in protein-protein interactions, and they raise the possibility of a similar involvement of the PAD of other Y family Pols in protein-protein interactions. We discuss the possible roles of Rev1 versus the Rev1-Rev7 complex in TLS.
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Affiliation(s)
- Narottam Acharya
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, 6.104 Blocker Medical Research Building, 11th and Mechanic Streets, Galveston, TX 77555-1061, USA
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43
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Haracska L, Johnson RE, Prakash L, Prakash S. Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA polymerase activity but no DNA polymerase activity. Mol Cell Biol 2005; 25:10183-9. [PMID: 16260630 PMCID: PMC1280283 DOI: 10.1128/mcb.25.22.10183-10189.2005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Saccharomyces cerevisiae Trf4 and Trf5 proteins are members of a distinct family of eukaryotic DNA polymerase beta-like nucleotidyltransferases, and a template-dependent DNA polymerase activity has been reported for Trf4. To define the nucleotidyltransferase activities associated with Trf4 and Tr5, we purified these proteins from yeast cells and show that whereas both proteins exhibit a robust poly(A) polymerase activity, neither of them shows any evidence of a DNA polymerase activity. The poly(A) polymerase activity, as determined for Trf4, is strictly Mn2+ dependent and highly ATP specific, incorporating AMP onto the free 3'-hydroxyl end of an RNA primer. Unlike the related poly(A) polymerases from other eukaryotes, which are located in the cytoplasm and regulate the stability and translation efficiency of specific mRNAs, the Trf4 and Trf5 proteins are nuclear, and a multiprotein complex associated with Trf4 has been recently shown to polyadenylate a variety of misfolded or inappropriately expressed RNAs which activate their degradation by the exosome. To account for the effects of Trf4/Trf5 proteins on the various aspects of DNA metabolism, including chromosome condensation, DNA replication, and sister chromatid cohesion, we suggest an additional and essential role for the Trf4 and Trf5 protein complexes in generating functional mRNA poly(A) tails in the nucleus.
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Affiliation(s)
- Lajos Haracska
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
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44
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Haracska L, Acharya N, Unk I, Johnson RE, Hurwitz J, Prakash L, Prakash S. A single domain in human DNA polymerase iota mediates interaction with PCNA: implications for translesion DNA synthesis. Mol Cell Biol 2005; 25:1183-90. [PMID: 15657443 PMCID: PMC544020 DOI: 10.1128/mcb.25.3.1183-1190.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA polymerases (Pols) of the Y family rescue stalled replication forks by promoting replication through DNA lesions. Humans have four Y family Pols, eta, iota, kappa, and Rev1, of which Pols eta, iota, and kappa have been shown to physically interact with proliferating cell nuclear antigen (PCNA) and be functionally stimulated by it. However, in sharp contrast to the large increase in processivity that PCNA binding imparts to the replicative Pol, Poldelta, the processivity of Y family Pols is not enhanced upon PCNA binding. Instead, PCNA binding improves the efficiency of nucleotide incorporation via a reduction in the apparent K(m) for the nucleotide. Here we show that Poliota interacts with PCNA via only one of its conserved PCNA binding motifs, regardless of whether PCNA is bound to DNA or not. The mode of PCNA binding by Poliota is quite unlike that in Poldelta, where multisite interactions with PCNA provide for a very tight binding of the replicating Pol with PCNA. We discuss the implications of these observations for the accuracy of DNA synthesis during translesion synthesis and for the process of Pol exchange at the lesion site.
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Affiliation(s)
- Lajos Haracska
- Sealy Center for Molecular Science, University of Texas Medical Branch, 6.104 Medical Research Building, 11th and Mechanic Streets, Galveston, TX 77555-1061, USA
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45
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Washington MT, Minko IG, Johnson RE, Haracska L, Harris TM, Lloyd RS, Prakash S, Prakash L. Efficient and error-free replication past a minor-groove N2-guanine adduct by the sequential action of yeast Rev1 and DNA polymerase zeta. Mol Cell Biol 2004; 24:6900-6. [PMID: 15282292 PMCID: PMC479736 DOI: 10.1128/mcb.24.16.6900-6906.2004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rev1, a member of the Y family of DNA polymerases, functions in lesion bypass together with DNA polymerase zeta (Pol zeta). Rev1 is a highly specialized enzyme in that it incorporates only a C opposite template G. While Rev1 plays an indispensable structural role in Pol zeta-dependent lesion bypass, the role of its DNA synthetic activity in lesion bypass has remained unclear. Since interactions of DNA polymerases with the DNA minor groove contribute to the nearly equivalent efficiencies and fidelities of nucleotide incorporation opposite each of the four template bases, here we examine the possibility that unlike other DNA polymerases, Rev1 does not come into close contact with the minor groove of the incipient base pair, and that enables it to incorporate a C opposite the N(2)-adducted guanines in DNA. To test this idea, we examined whether Rev1 could incorporate a C opposite the gamma-hydroxy-1,N(2)-propano-2'deoxyguanosine DNA minor-groove adduct, which is formed from the reaction of acrolein with the N(2) of guanine. Acrolein, an alpha,beta-unsaturated aldehyde, is generated in vivo as the end product of lipid peroxidation and from other oxidation reactions. We show here that Rev1 efficiently incorporates a C opposite this adduct from which Pol zeta subsequently extends, thereby completing the lesion bypass reaction. Based upon these observations, we suggest that an important role of the Rev1 DNA synthetic activity in lesion bypass is to incorporate a C opposite the various N(2)-guanine DNA minor-groove adducts that form in DNA.
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Affiliation(s)
- M Todd Washington
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, 77555-1061, USA
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46
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Guzder SN, Torres-Ramos C, Johnson RE, Haracska L, Prakash L, Prakash S. Requirement of yeast Rad1-Rad10 nuclease for the removal of 3'-blocked termini from DNA strand breaks induced by reactive oxygen species. Genes Dev 2004; 18:2283-91. [PMID: 15371342 PMCID: PMC517521 DOI: 10.1101/gad.1232804] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Rad1-Rad10 nuclease of yeast and its human counterpart ERCC1-XPF are indispensable for nucleotide excision repair, where they act by cleaving the damaged DNA strand on the 5'-side of the lesion. Intriguingly, the ERCC1- and XPF-deficient mice show a severe postnatal growth defect and they die at approximately 3 wk after birth. Here we present genetic and biochemical evidence for the requirement of Rad1-Rad10 nuclease in the removal of 3'-blocked termini from DNA strand breaks induced on treatment of yeast cells with the oxidative DNA damaging agent H(2)O(2). Our genetic studies indicate that 3'-blocked termini are removed in yeast by the three competing pathways that involve the Apn1, Apn2, and Rad1-Rad10 nucleases, and we show that the Rad1-Rad10 nuclease proficiently cleaves DNA modified with a 3'-phosphoglycolate terminus. From these observations, we infer that deficient removal of 3'-blocking groups formed from the action of oxygen free radicals generated during normal cellular metabolism is the primary underlying cause of the inviability of apn1Delta apn2Delta rad1Delta and apn1Deltaapn2Delta rad10Delta mutants and that such a deficiency accounts also for the severe growth defects of ERCC1- and XPF-deficient mice.
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Affiliation(s)
- Sami N Guzder
- Sealy Center for Molelcular Science, University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1061, USA
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Haracska L, Torres-Ramos CA, Johnson RE, Prakash S, Prakash L. Opposing effects of ubiquitin conjugation and SUMO modification of PCNA on replicational bypass of DNA lesions in Saccharomyces cerevisiae. Mol Cell Biol 2004; 24:4267-74. [PMID: 15121847 PMCID: PMC400445 DOI: 10.1128/mcb.24.10.4267-4274.2004] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Rad6-Rad18 ubiquitin-conjugating enzyme complex of Saccharomyces cerevisiae promotes replication through DNA lesions via three separate pathways that include translesion synthesis (TLS) by DNA polymerases zeta (Polzeta) and Poleta and postreplicational repair mediated by the Mms2-Ubc13 ubiquitin-conjugating enzyme and Rad5. Here we report our studies with a proliferating cell nuclear antigen (PCNA) mutation, pol30-119, which results from a change of the lysine 164 residue to arginine. It has been shown recently that following treatment of yeast cells with DNA-damaging agents, the lysine 164 residue of PCNA becomes monoubiquitinated in a Rad6-Rad18-dependent manner and that subsequently this PCNA residue is polyubiquitinated via a lysine 63-linked ubiquitin chain in an Mms2-Ubc13-, Rad5-dependent manner. PCNA is also modified by SUMO conjugation at the lysine 164 residue. Our genetic studies with the pol30-119 mutation show that in addition to conferring a defect in Polzeta-dependent UV mutagenesis and in Poleta-dependent TLS, this PCNA mutation inhibits postreplicational repair of discontinuities that form in the newly synthesized strand across from UV lesions. In addition, we provide evidence for the activation of the RAD52 recombinational pathway in the pol30-119 mutant and we infer that SUMO conjugation at the lysine 164 residue of PCNA has a role in suppressing the Rad52-dependent postreplicational repair pathway.
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Affiliation(s)
- Lajos Haracska
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, Texas 77555-1061, USA
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48
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Haracska L, Prakash L, Prakash S. A mechanism for the exclusion of low-fidelity human Y-family DNA polymerases from base excision repair. Genes Dev 2003; 17:2777-85. [PMID: 14630940 PMCID: PMC280626 DOI: 10.1101/gad.1146103] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2003] [Accepted: 09/24/2003] [Indexed: 11/24/2022]
Abstract
The human Y-family DNA polymerases, Poliota, Poleta, and Polkappa, function in promoting replication through DNA lesions. However, because of their low fidelity, any involvement of these polymerases in DNA synthesis during base excision repair (BER) would be highly mutagenic. Mechanisms, therefore, must exist to exclude their participation in BER. Here, we show that although Poliota, Poleta, and Polkappa are all able to form a covalent Schiff base intermediate with the 5'-deoxyribose phosphate (5'-dRP) residue that results from the incision of DNA at an abasic site by an AP endonuclease, they all lack the ability for the subsequent catalytic removal of the 5'-dRP group. Instead, the covalent trapping of these polymerases by the 5'-dRP residue inhibits their DNA synthetic activity during BER. The unprecedented ability of these polymerases for robust Schiff base formation without the release of the 5'-dRP product provides a means of preventing their participation in the DNA synthetic step of BER, thereby avoiding the high incidence of mutagenesis and carcinogenesis that would otherwise occur.
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Affiliation(s)
- Lajos Haracska
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1061, USA
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49
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Prakash S, Johnson RE, Washington MT, Haracska L, Kondratick CM, Prakash L. Role of yeast and human DNA polymerase eta in error-free replication of damaged DNA. Cold Spring Harb Symp Quant Biol 2003; 65:51-9. [PMID: 12760020 DOI: 10.1101/sqb.2000.65.51] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- S Prakash
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, Texas 77555-1061, USA
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50
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Szlanka T, Haracska L, Kiss I, Deák P, Kurucz E, Andó I, Virágh E, Udvardy A. Deletion of proteasomal subunit S5a/Rpn10/p54 causes lethality, multiple mitotic defects and overexpression of proteasomal genes in Drosophila melanogaster. J Cell Sci 2003; 116:1023-33. [PMID: 12584246 DOI: 10.1242/jcs.00332] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The regulatory complex of the 26S proteasome is responsible for the selective recognition and binding of multiubiquitinated proteins. It was earlier shown that the subunit S5a/Rpn10/p54 of the regulatory complex is the only cellular protein capable of binding multiubiquitin chains in an in vitro overlay assay. The role of this subunit in substrate selection, however, is a subject of debate, following the observation that its deletion in Saccharomyces cerevisiae is not lethal and instead causes only a mild phenotype. To study the function of this subunit in higher eukaryotes, a mutant Drosophila strain was constructed by deleting the single copy gene encoding subunit S5a/Rpn10/p54. This deletion caused larval-pupal polyphasic lethality, multiple mitotic defects, the accumulation of higher multimers of ubiquitinated proteins and a huge accumulation of defective 26S proteasome particles. Deletion of the subunit S5a/Rpn10/p54 does not destabilise the regulatory complex and does not disturb the assembly of the regulatory complex and the catalytic core. The pupal lethality is a consequence of the depletion of the maternally provided 26S proteasome during the larval stages and a sudden increase in the proteasomal activity demands during the first few hours of pupal development. The huge accumulation of the fully assembled 26S proteasome in the deletion mutant and the lack of free subunits or partially assembled particles indicate that there is a highly coordinated accumulation of all the subunits of the 26S proteasome. This suggests that in higher eukaryotes, as with yeast, a feedback circuit coordinately regulates the expression of the proteasomal genes, and this adjusts the actual proteasome concentration in the cells according to the temporal and/or spatial proteolytic demands.
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Affiliation(s)
- Tamás Szlanka
- Biological Research Center of the Hungarian Academy of Sciences, H-6701 Szeged, P.O. Box 521, Hungary
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