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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Verma I, Chhatlani K, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae. iScience 2024; 27:110012. [PMID: 38868188 PMCID: PMC11166700 DOI: 10.1016/j.isci.2024.110012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/15/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered orthologs of the human RNASEH2A-G37S and RNASEH2C-R69W AGS mutations in yeast Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these AGS-ortholog mutants. We found a high rNMP presence in the nuclear genome of rnh201-G42S-mutant cells, and an elevated rCMP content in both mutants, reflecting preferential cleavage of RNase H2 at rGMP. We discovered unique rNMP patterns in each mutant, showing differential activity of the AGS mutants on the leading or lagging replication strands. This study guides future research on rNMP characteristics in human genomes with AGS mutations.
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Affiliation(s)
- Deepali L. Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L. Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ishika Verma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kirti Chhatlani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Zeel H. Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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2
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Yoon J, Lee J, Kim J, Lee SM, Kim S, Park HG. A novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension reaction. Biosens Bioelectron 2024; 253:116174. [PMID: 38432074 DOI: 10.1016/j.bios.2024.116174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
We herein present a novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction. The detection probe employed as a key component in this technique serves as a substrate for RNase H and triggers the PS-THSP reaction upon the RNase H-mediated degradation of the probe. As a consequence, a large number of long concatemeric amplification products could be produced and used to identify the RNase H activity through the fluorescence signals produced by the nucleic acid-specific fluorescent dye, SYTO 9. Importantly, the use of the gp32 protein allowed the PS-THSP reaction to be performed at 37 °C, ultimately enabling an isothermal one-step RNase H assay. Based on this sophisticated design principle, the RNase H activity was very sensitively detected, down to 0.000237 U mL-1 with high specificity. We further verified its practical applicability through its successful application to the screening of RNase H inhibitors. With its operational convenience and excellent analytical performance, this technique could serve as a new platform for RNase H assay in a wide range of biological applications.
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Affiliation(s)
- Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jinhwan Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jaemin Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Mo Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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3
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Grasso L, Fonzino A, Manzari C, Leonardi T, Picardi E, Gissi C, Lazzaro F, Pesole G, Muzi-Falconi M. Detection of ribonucleotides embedded in DNA by Nanopore sequencing. Commun Biol 2024; 7:491. [PMID: 38654143 DOI: 10.1038/s42003-024-06077-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome instability and human pathologies are not fully understood. The available sequencing technologies only allow to indirectly deduce the genomic location of rNMPs. Oxford Nanopore Technologies (ONT) may overcome such limitation, revealing the sites of rNMPs incorporation in genomic DNA directly from raw sequencing signals. We synthesized two types of DNA molecules containing rNMPs at known or random positions and we developed data analysis pipelines for DNA-embedded ribonucleotides detection by ONT. We report that ONT can identify all four ribonucleotides incorporated in DNA by capturing rNMPs-specific alterations in nucleotide alignment features, current intensity, and dwell time. We propose that ONT may be successfully employed to directly map rNMPs in genomic DNA and we suggest a strategy to build an ad hoc basecaller to analyse native genomes.
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Affiliation(s)
- Lavinia Grasso
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Adriano Fonzino
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
| | - Caterina Manzari
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139, Milano, Italy
| | - Ernesto Picardi
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70126, Bari, Italy
| | - Carmela Gissi
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70126, Bari, Italy
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy.
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70126, Bari, Italy.
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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4
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Krawic C, Luczak MW, Valiente S, Zhitkovich A. Atypical genotoxicity of carcinogenic nickel(II): Linkage to dNTP biosynthesis, DNA-incorporated rNMPs, and impaired repair of TOP1-DNA crosslinks. J Biol Chem 2023; 299:105385. [PMID: 37890780 PMCID: PMC10692736 DOI: 10.1016/j.jbc.2023.105385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Cancer is a genetic disease requiring multiple mutations for its development. However, many carcinogens are DNA-unreactive and nonmutagenic and consequently described as nongenotoxic. One of such carcinogens is nickel, a global environmental pollutant abundantly emitted by burning of coal. We investigated activation of DNA damage responses by Ni and identified this metal as a replication stressor. Genotoxic stress markers indicated the accumulation of ssDNA and stalled replication forks, and Ni-treated cells were dependent on ATR for suppression of DNA damage and long-term survival. Replication stress by Ni resulted from destabilization of RRM1 and RRM2 subunits of ribonucleotide reductase and the resulting deficiency in dNTPs. Ni also increased DNA incorporation of rNMPs (detected by a specific fluorescent assay) and strongly enhanced their genotoxicity as a result of repressed repair of TOP1-DNA protein crosslinks (TOP1-DPC). The DPC-trap assay found severely impaired SUMOylation and K48-polyubiquitination of DNA-crosslinked TOP1 due to downregulation of specific enzymes. Our findings identified Ni as the human carcinogen inducing genome instability via DNA-embedded ribonucleotides and accumulation of TOP1-DPC which are carcinogenic abnormalities with poor detectability by the standard mutagenicity tests. The discovered mechanisms for Ni could also play a role in genotoxicity of other protein-reactive carcinogens.
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Affiliation(s)
- Casey Krawic
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Michal W Luczak
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Sophia Valiente
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA.
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5
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Heuzé J, Kemiha S, Barthe A, Vilarrubias AT, Aouadi E, Aiello U, Libri D, Lin Y, Lengronne A, Poli J, Pasero P. RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart. EMBO J 2023; 42:e113104. [PMID: 37855233 PMCID: PMC10690446 DOI: 10.15252/embj.2022113104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.
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Affiliation(s)
- Jonathan Heuzé
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Samira Kemiha
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Antoine Barthe
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Alba Torán Vilarrubias
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Elyès Aouadi
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Present address:
Institut de Génétique Moléculaire de MontpellierUniversité de Montpellier, CNRSMontpellierFrance
| | - Yea‐Lih Lin
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Armelle Lengronne
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Jérôme Poli
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Philippe Pasero
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
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6
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Tsao N, Ashour ME, Mosammaparast N. How RNA impacts DNA repair. DNA Repair (Amst) 2023; 131:103564. [PMID: 37776841 PMCID: PMC11232704 DOI: 10.1016/j.dnarep.2023.103564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 10/02/2023]
Abstract
The central dogma of molecular biology posits that genetic information flows unidirectionally, from DNA, to RNA, and finally to protein. However, this directionality is broken in some cases, such as reverse transcription where RNA is converted to DNA by retroviruses and certain transposable elements. Our genomes have evolved and adapted to the presence of reverse transcription. Similarly, our genome is continuously maintained by several repair pathways to reverse damage due to various endogenous and exogenous sources. More recently, evidence has revealed that RNA, while in certain contexts may be detrimental for genome stability, is involved in promoting certain types of DNA repair. Depending on the pathway in question, the size of these DNA repair-associated RNAs range from one or a few ribonucleotides to long fragments of RNA. Moreover, RNA is highly modified, and RNA modifications have been revealed to be functionally associated with specific DNA repair pathways. In this review, we highlight aspects of this unexpected layer of genomic maintenance, demonstrating how RNA may influence DNA integrity.
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Affiliation(s)
- Ning Tsao
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mohamed E Ashour
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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7
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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560505. [PMID: 37873120 PMCID: PMC10592897 DOI: 10.1101/2023.10.02.560505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered two AGS-ortholog mutations in Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these yeast AGS-ortholog mutants. We found higher rNMP incorporation in the nuclear genome of rnh201-G42S than in wild-type and rnh203-K46W-mutant cells, and an elevated rCMP content in both mutants. Moreover, we uncovered unique rNMP patterns in each mutant, highlighting a differential activity of the AGS mutants towards rNMPs embedded on the leading or on the lagging strand of DNA replication. This study guides future research on rNMP characteristics in human genomic samples carrying AGS mutations.
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Affiliation(s)
- Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Zeel H Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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8
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Heuzé J, Lin YL, Lengronne A, Poli J, Pasero P. Impact of R-loops on oncogene-induced replication stress in cancer cells. C R Biol 2023; 346:95-105. [PMID: 37779381 DOI: 10.5802/crbiol.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 10/03/2023]
Abstract
Replication stress is an alteration in the progression of replication forks caused by a variety of events of endogenous or exogenous origin. In precancerous lesions, this stress is exacerbated by the deregulation of oncogenic pathways, which notably disrupts the coordination between replication and transcription, and leads to genetic instability and cancer development. It is now well established that transcription can interfere with genome replication in different ways, such as head-on collisions between polymerases, accumulation of positive DNA supercoils or formation of R-loops. These structures form during transcription when nascent RNA reanneals with DNA behind the RNA polymerase, forming a stable DNA:RNA hybrid. In this review, we discuss how these different cotranscriptional processes disrupt the progression of replication forks and how they contribute to genetic instability in cancer cells.
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9
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Tripathi D, Oldenburg DJ, Bendich AJ. Ribonucleotide and R-Loop Damage in Plastid DNA and Mitochondrial DNA during Maize Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3161. [PMID: 37687407 PMCID: PMC10489836 DOI: 10.3390/plants12173161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Although the temporary presence of ribonucleotides in DNA is normal, their persistence represents a form of DNA damage. Here, we assess such damage and damage defense to DNA in plastids and mitochondria of maize. Shoot development proceeds from meristematic, non-pigmented cells containing proplastids and promitochondria at the leaf base to non-dividing green cells in the leaf blade containing mature organelles. The organellar DNAs (orgDNAs) become fragmented during this transition. Previously, orgDNA damage and damage defense of two types, oxidative and glycation, was described in maize, and now a third type, ribonucleotide damage, is reported. We hypothesized that ribonucleotide damage changes during leaf development and could contribute to the demise of orgDNAs. The levels of ribonucleotides and R-loops in orgDNAs and of RNase H proteins in organelles were measured throughout leaf development and in leaves grown in light and dark conditions. The data reveal that ribonucleotide damage to orgDNAs increased by about 2- to 5-fold during normal maize development from basal meristem to green leaf and when leaves were grown in normal light conditions compared to in the dark. During this developmental transition, the levels of the major agent of defense, RNase H, declined. The decline in organellar genome integrity during maize development may be attributed to oxidative, glycation, and ribonucleotide damages that are not repaired.
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Affiliation(s)
| | | | - Arnold J. Bendich
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (D.T.); (D.J.O.)
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10
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Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A, Luke B. Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun 2023; 14:1227. [PMID: 36869098 PMCID: PMC9984532 DOI: 10.1038/s41467-023-36866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Single ribonucleoside monophosphates (rNMPs) are transiently present in eukaryotic genomes. The RNase H2-dependent ribonucleotide excision repair (RER) pathway ensures error-free rNMP removal. In some pathological conditions, rNMP removal is impaired. If these rNMPs hydrolyze during, or prior to, S phase, toxic single-ended double-strand breaks (seDSBs) can occur upon an encounter with replication forks. How such rNMP-derived seDSB lesions are repaired is unclear. We expressed a cell cycle phase restricted allele of RNase H2 to nick at rNMPs in S phase and study their repair. Although Top1 is dispensable, the RAD52 epistasis group and Rtt101Mms1-Mms22 dependent ubiquitylation of histone H3 become essential for rNMP-derived lesion tolerance. Consistently, loss of Rtt101Mms1-Mms22 combined with RNase H2 dysfunction leads to compromised cellular fitness. We refer to this repair pathway as nick lesion repair (NLR). The NLR genetic network may have important implications in the context of human pathologies.
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Affiliation(s)
- Natalie Schindler
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Matthias Tonn
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Vanessa Kellner
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Department of Biology, New York University, New York, NY, USA
| | - Jia Jun Fung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Arianna Lockhart
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Olga Vydzhak
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefanie Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anton Khmelinskii
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Brian Luke
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany. .,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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11
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RNA:DNA hybrids from Okazaki fragments contribute to establish the Ku-mediated barrier to replication-fork degradation. Mol Cell 2023; 83:1061-1074.e6. [PMID: 36868227 DOI: 10.1016/j.molcel.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/09/2022] [Accepted: 02/04/2023] [Indexed: 03/05/2023]
Abstract
Nonhomologous end-joining (NHEJ) factors act in replication-fork protection, restart, and repair. Here, we identified a mechanism related to RNA:DNA hybrids to establish the NHEJ factor Ku-mediated barrier to nascent strand degradation in fission yeast. RNase H activities promote nascent strand degradation and replication restart, with a prominent role of RNase H2 in processing RNA:DNA hybrids to overcome the Ku barrier to nascent strand degradation. RNase H2 cooperates with the MRN-Ctp1 axis to sustain cell resistance to replication stress in a Ku-dependent manner. Mechanistically, the need of RNaseH2 in nascent strand degradation requires the primase activity that allows establishing the Ku barrier to Exo1, whereas impairing Okazaki fragment maturation reinforces the Ku barrier. Finally, replication stress induces Ku foci in a primase-dependent manner and favors Ku binding to RNA:DNA hybrids. We propose a function for the RNA:DNA hybrid originating from Okazaki fragments in controlling the Ku barrier specifying nuclease requirement to engage fork resection.
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12
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Eghbalsaied S, Kues WA. CRISPR/Cas9-mediated targeted knock-in of large constructs using nocodazole and RNase HII. Sci Rep 2023; 13:2690. [PMID: 36792645 PMCID: PMC9931768 DOI: 10.1038/s41598-023-29789-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
On-target integration of large cassettes via homology-directed repair (HDR) has several applications. However, the HDR-mediated targeted knock-in suffered from low efficiency. In this study, we made several large plasmids (12.1-13.4 kb) which included the CRISPR/Cas9 system along with a puromycin transgene as part of the large DNA donor (5.3-7.1 kb insertion cassettes) and used them to evaluate their targeted integration efficiency into a transgenic murine embryonic fibroblast (MEF) cell line carrying a single copy of a Venus transgene. We established a detection assay by which HDR events could be discriminated from the error-prone non-homologous end-joining (NHEJ) events. Improving the plasmid quality could considerably leverage the cell toxicity impediment of large plasmids. The use of the TILD (targeted integration with linearized dsDNA) cassettes did not improve the HDR rate compared to the circular plasmids. However, the direct inclusion of nocodazole into the electroporation solution significantly improved the HDR rate. Also, simultaneous delivery of RNase HII and the donor plasmids into the electroporated cells considerably improved the HDR events. In conclusion, the results of this study showed that using cell synchronization reagents in the electroporation medium can efficiently induce HDR rate in the mammalian genome.
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Affiliation(s)
- Shahin Eghbalsaied
- grid.417834.dBiotechnology/Stem Cell Physiology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Höltystr. 10, 31535 Neustadt, Germany ,grid.411463.50000 0001 0706 2472Department of Animal Science, Isfahan (Khorasgan) Branch, Islamic Azad University, Tehran, Iran ,grid.1008.90000 0001 2179 088XSchool of Biosciences, Royal Parade, The University of Melbourne, Melbourne, VIC Australia
| | - Wilfried A. Kues
- grid.417834.dBiotechnology/Stem Cell Physiology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Höltystr. 10, 31535 Neustadt, Germany
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13
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McPherson KS, Rizzo AA, Erlandsen H, Chatterjee N, Walker GC, Korzhnev DM. Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ. J Biol Chem 2023; 299:102859. [PMID: 36592930 PMCID: PMC9926120 DOI: 10.1016/j.jbc.2022.102859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023] Open
Abstract
Translesion synthesis (TLS) DNA polymerase Polζ is crucial for the bypass replication over sites of DNA damage. The Rev7 subunit of Polζ is a HORMA (Hop1, Rev7, Mad2) protein that facilitates recruitment of Polζ to the replication fork via interactions with the catalytic subunit Rev3 and the translesion synthesis scaffold protein Rev1. Human Rev7 (hRev7) interacts with two Rev7-binding motifs (RBMs) of hRev3 by a mechanism conserved among HORMA proteins whereby the safety-belt loop of hRev7 closes on the top of the ligand. The two copies of hRev7 tethered by the two hRev3-RBMs form a symmetric head-to-head dimer through the canonical HORMA dimerization interface. Recent cryo-EM structures reveal that Saccharomyces cerevisiae Polζ (scPolζ) also includes two copies of scRev7 bound to distinct regions of scRev3. Surprisingly, the HORMA dimerization interface is not conserved in scRev7, with the two scRev7 protomers forming an asymmetric head-to-tail dimer with a much smaller interface than the hRev7 dimer. Here, we validated the two adjacent RBM motifs in scRev3, which bind scRev7 with affinities that differ by two orders of magnitude and confirmed the 2:1 stoichiometry of the scRev7:Rev3 complex in solution. However, our biophysical studies reveal that scRev7 does not form dimers in solution either on its own accord or when tethered by the two RBMs in scRev3. These findings imply that the scRev7 dimer observed in the cryo-EM structures is induced by scRev7 interactions with other Polζ subunits and that Rev7 homodimerization via the HORMA interface is a mechanism that emerged later in evolution.
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Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Alessandro A Rizzo
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment, University of Connecticut, Storrs, Connecticut, USA
| | - Nimrat Chatterjee
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
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14
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Pang J, Guo Q, Lu Z. The catalytic mechanism, metal dependence, substrate specificity, and biodiversity of ribonuclease H. Front Microbiol 2022; 13:1034811. [PMID: 36478866 PMCID: PMC9719913 DOI: 10.3389/fmicb.2022.1034811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2023] Open
Abstract
Ribonucleoside monophosphates are inevitably misincorporated into the DNA genome inside cells, and they need to be excised to avoid chromosome instability. Ribonucleases H (RNases H) are enzymes that specifically hydrolyze the RNA strand of RNA/DNA hybrids or the RNA moiety from DNA containing a stretch of RNA, they therefore are required for DNA integrity. Extensive studies have drawn a mostly clear picture of the mechanisms of RNase H catalysis, but some questions are still lacking definitive answers. This review summarizes three alternative models of RNase H catalysis. The two-metal model is prevalent, but a three-metal model suggests the involvement of a third cation in catalysis. Apparently, the mechanisms underlying metal-dependent hydrolyzation are more complicated than initially thought. We also discuss the metal choices of RNases H and analyze how chemically similar cations function differently. Substrate and cleavage-site specificities vary among RNases H, and this is explicated in detail. An intriguing phenomenon is that organisms have diverse RNase H combinations, which may provide important hints to how rnh genes were transferred during evolution. Whether RNase H is essential for cellular growth, a key question in the study of in vivo functions, is also discussed. This article may aid in understanding the mechanisms underlying RNase H and in developing potentially promising applications of it.
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Affiliation(s)
| | | | - Zheng Lu
- Department of Biology, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
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15
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Raducanu VS, Tehseen M, Al-Amodi A, Joudeh LI, De Biasio A, Hamdan SM. Mechanistic investigation of human maturation of Okazaki fragments reveals slow kinetics. Nat Commun 2022; 13:6973. [PMID: 36379932 PMCID: PMC9666535 DOI: 10.1038/s41467-022-34751-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The final steps of lagging strand synthesis induce maturation of Okazaki fragments via removal of the RNA primers and ligation. Iterative cycles between Polymerase δ (Polδ) and Flap endonuclease-1 (FEN1) remove the primer, with an intermediary nick structure generated for each cycle. Here, we show that human Polδ is inefficient in releasing the nick product from FEN1, resulting in non-processive and remarkably slow RNA removal. Ligase 1 (Lig1) can release the nick from FEN1 and actively drive the reaction toward ligation. These mechanisms are coordinated by PCNA, which encircles DNA, and dynamically recruits Polδ, FEN1, and Lig1 to compete for their substrates. Our findings call for investigating additional pathways that may accelerate RNA removal in human cells, such as RNA pre-removal by RNase Hs, which, as demonstrated herein, enhances the maturation rate ~10-fold. They also suggest that FEN1 may attenuate the various activities of Polδ during DNA repair and recombination.
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Affiliation(s)
- Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Amani Al-Amodi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Luay I Joudeh
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Alfredo De Biasio
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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16
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Sui Y, Epstein A, Dominska M, Zheng DQ, Petes T, Klein H. Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides. Nucleic Acids Res 2022; 50:6890-6902. [PMID: 35748861 PMCID: PMC9262587 DOI: 10.1093/nar/gkac536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Ribonucleotides can be incorporated into DNA during replication by the replicative DNA polymerases. These aberrant DNA subunits are efficiently recognized and removed by Ribonucleotide Excision Repair, which is initiated by the heterotrimeric enzyme RNase H2. While RNase H2 is essential in higher eukaryotes, the yeast Saccharomyces cerevisiae can survive without RNase H2 enzyme, although the genome undergoes mutation, recombination and other genome instability events at an increased rate. Although RNase H2 can be considered as a protector of the genome from the deleterious events that can ensue from recognition and removal of embedded ribonucleotides, under conditions of high ribonucleotide incorporation and retention in the genome in a RNase H2-negative strain, sudden introduction of active RNase H2 causes massive DNA breaks and genome instability in a condition which we term 'ribodysgenesis'. The DNA breaks and genome instability arise solely from RNase H2 cleavage directed to the ribonucleotide-containing genome. Survivors of ribodysgenesis have massive loss of heterozygosity events stemming from recombinogenic lesions on the ribonucleotide-containing DNA, with increases of over 1000X from wild-type. DNA breaks are produced over one to two divisions and subsequently cells adapt to RNase H2 and ribonucleotides in the genome and grow with normal levels of genome instability.
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Affiliation(s)
- Yang Sui
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan 316021, China,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anastasiya Epstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dao-Qiong Zheng
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan 316021, China,Hainan Institute of Zhejiang University, Sanya 572000, China,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hannah L Klein
- To whom correspondence should be addressed. Tel: +1 212 263 5778;
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17
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Xie Z, Chen S, Zhang W, Zhao S, Zhao Z, Wang X, Huang Y, Yi G. A novel fluorescence amplification strategy combining cascade primer exchange reaction with CRISPR/Cas12a system for ultrasensitive detection of RNase H activity. Biosens Bioelectron 2022; 206:114135. [DOI: 10.1016/j.bios.2022.114135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 12/16/2022]
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18
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Williams JS, Kunkel TA. Ribonucleotide Incorporation by Eukaryotic B-family Replicases and Its Implications for Genome Stability. Annu Rev Biochem 2022; 91:133-155. [PMID: 35287470 DOI: 10.1146/annurev-biochem-032620-110354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our current view of how DNA-based genomes are efficiently and accurately replicated continues to evolve as new details emerge on the presence of ribonucleotides in DNA. Ribonucleotides are incorporated during eukaryotic DNA replication at rates that make them the most common noncanonical nucleotide placed into the nuclear genome, they are efficiently repaired, and their removal impacts genome integrity. This review focuses on three aspects of this subject: the incorporation of ribonucleotides into the eukaryotic nuclear genome during replication by B-family DNA replicases, how these ribonucleotides are removed, and the consequences of their presence or removal for genome stability and disease. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
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19
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Galati E, Bosio MC, Novarina D, Chiara M, Bernini GM, Mozzarelli AM, García-Rubio ML, Gómez-González B, Aguilera A, Carzaniga T, Todisco M, Bellini T, Nava GM, Frigè G, Sertic S, Horner DS, Baryshnikova A, Manzari C, D'Erchia AM, Pesole G, Brown GW, Muzi-Falconi M, Lazzaro F. VID22 counteracts G-quadruplex-induced genome instability. Nucleic Acids Res 2021; 49:12785-12804. [PMID: 34871443 PMCID: PMC8682794 DOI: 10.1093/nar/gkab1156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
Genome instability is a condition characterized by the accumulation of genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways affecting endogenous DNA damage and genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, reported to be involved in DNA double-strand break repair. vid22Δ cells exhibit increased levels of endogenous DNA damage, chronic DNA damage response activation and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. Vid22 binds to and protects DNA at G4-containing regions both in vitro and in vivo. Loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. Moreover, the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism.
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Affiliation(s)
- Elena Galati
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Maria C Bosio
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Daniele Novarina
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.,Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Giulia M Bernini
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alessandro M Mozzarelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Maria L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Vanvitelli 32, 20129 Milan, Italy
| | - Marco Todisco
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Vanvitelli 32, 20129 Milan, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Vanvitelli 32, 20129 Milan, Italy
| | - Giulia M Nava
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sarah Sertic
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - David S Horner
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.,Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Anastasia Baryshnikova
- Department of Molecular Genetics and Donnelly Centre, University of Toronto, Toronto, Canada
| | - Caterina Manzari
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Anna M D'Erchia
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari 'A. Moro', Bari, Italy
| | - Graziano Pesole
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari 'A. Moro', Bari, Italy
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Ontario M5S 3E1, Toronto, Canada
| | - Marco Muzi-Falconi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Federico Lazzaro
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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20
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Hu Y, Xie Q, Chang L, Tao X, Tong C, Liu B, Wang W. A radar-like DNA monitor for RNase H-targeted natural compounds screening and RNase H activity in situ detection. Analyst 2021; 146:5980-5987. [PMID: 34499070 DOI: 10.1039/d1an01046h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ribonuclease H is essential for the research and development of complex pathema. The high rigidity and versatility of DNA tetrahedrons means they are often used in biosensing systems. Inspired by "radar" technology, we proposed a radar-like monitor to detect RNase H activity in vitro and in situ by integrating DNA tetrahedral elements. The structure of a radar-like monitor was self-assembled from five customized single nucleic acid strands. Four DNA strands were assembled as DNA tetrahedrons with a long strand labeled by Dabcyl (quencher) at one of the apexes, while the fifth strand (DNA-RNA heterozygous strand) was labeled with a FAM (Fluorophore) hybrid with a long strand. The fluorescence was quenched because the fluorophore and the quencher were very close. In the presence of RNase H, the RNA chain was hydrolyzed and the fluorophore released, resulting in fluorescence recovery. The radar-like monitor was used to detect the RNase H activity in vitro with a detection limit of 0.01 U mL-1. Based on the RNase H activity detection and the inhibitory effect of natural-compounds-targeting RNase H, three inhibitors were obtained among 35 compounds extracted from Panax japonicus. Therefore, the radar-like monitor was successfully used to detect RNase H activity in situ due to the long-term anti-DNase I effect of the RNA/DNA hybrid structure and DNA tetrahedrons structure. Overall, this radar-like monitor can effectively avoid false-positive signals and significantly improve the accuracy, precision, and reliability of detection. It is expected that the development of such an intelligent nano-platform will open the door to cancer diagnosis and treatment in clinical systems.
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Affiliation(s)
- Yalei Hu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.
| | - Qian Xie
- TCM and Ethnomedicine Innovation & Development International Laboratory, Innovative Material Medical Research Institute, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China.
| | - Li Chang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410008, PR China
| | - Xueqing Tao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.
| | - Chunyi Tong
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.
| | - Bin Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Innovative Material Medical Research Institute, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China.
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21
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Elserafy M, El-Shiekh I, Fleifel D, Atteya R, AlOkda A, Abdrabbou MM, Nasr M, El-Khamisy SF. A role for Rad5 in ribonucleoside monophosphate (rNMP) tolerance. Life Sci Alliance 2021; 4:4/10/e202000966. [PMID: 34407997 PMCID: PMC8380674 DOI: 10.26508/lsa.202000966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 07/24/2021] [Accepted: 07/03/2021] [Indexed: 11/29/2022] Open
Abstract
Ribonucleoside incorporation in genomic DNA poses a significant threat to genomic integrity. Here, we describe how cells tolerate this threat and discuss implications for cancer therapeutics. Ribonucleoside monophosphate (rNMP) incorporation in genomic DNA poses a significant threat to genomic integrity. In addition to repair, DNA damage tolerance mechanisms ensure replication progression upon encountering unrepaired lesions. One player in the tolerance mechanism is Rad5, which is an E3 ubiquitin ligase and helicase. Here, we report a new role for yeast Rad5 in tolerating rNMP incorporation, in the absence of the bona fide ribonucleotide excision repair pathway via RNase H2. This role of Rad5 is further highlighted after replication stress induced by hydroxyurea or by increasing rNMP genomic burden using a mutant DNA polymerase (Pol ε - Pol2-M644G). We further demonstrate the importance of the ATPase and ubiquitin ligase domains of Rad5 in rNMP tolerance. These findings suggest a similar role for the human Rad5 homologues helicase-like transcription factor (HLTF) and SNF2 Histone Linker PHD RING Helicase (SHPRH) in rNMP tolerance, which may impact the response of cancer cells to replication stress-inducing therapeutics.
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Affiliation(s)
- Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Dalia Fleifel
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Reham Atteya
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Abdelrahman AlOkda
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed M Abdrabbou
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mostafa Nasr
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Sherif F El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt .,The Healthy Lifespan Institute and Institute of Neuroscience, School of Bioscience, University of Sheffield, South Yorkshire, UK.,The Institute of Cancer Therapeutics, University of Bradford, West Yorkshire, UK.,Center for Genomics, Zewail City of Science and Technology, Giza, Egypt
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22
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Chen XS, Pomerantz RT. DNA Polymerase θ: A Cancer Drug Target with Reverse Transcriptase Activity. Genes (Basel) 2021; 12:1146. [PMID: 34440316 PMCID: PMC8391894 DOI: 10.3390/genes12081146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of precision medicine from the development of Poly (ADP-ribose) polymerase (PARP) inhibitors that preferentially kill cells defective in homologous recombination has sparked wide interest in identifying and characterizing additional DNA repair enzymes that are synthetic lethal with HR factors. DNA polymerase theta (Polθ) is a validated anti-cancer drug target that is synthetic lethal with HR factors and other DNA repair proteins and confers cellular resistance to various genotoxic cancer therapies. Since its initial characterization as a helicase-polymerase fusion protein in 2003, many exciting and unexpected activities of Polθ in microhomology-mediated end-joining (MMEJ) and translesion synthesis (TLS) have been discovered. Here, we provide a short review of Polθ's DNA repair activities and its potential as a drug target and highlight a recent report that reveals Polθ as a naturally occurring reverse transcriptase (RT) in mammalian cells.
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Affiliation(s)
- Xiaojiang S. Chen
- Molecular and Computational Biology, USC Dornsife Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Richard T. Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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23
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Palancade B, Rothstein R. The Ultimate (Mis)match: When DNA Meets RNA. Cells 2021; 10:cells10061433. [PMID: 34201169 PMCID: PMC8227541 DOI: 10.3390/cells10061433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/20/2022] Open
Abstract
RNA-containing structures, including ribonucleotide insertions, DNA:RNA hybrids and R-loops, have recently emerged as critical players in the maintenance of genome integrity. Strikingly, different enzymatic activities classically involved in genome maintenance contribute to their generation, their processing into genotoxic or repair intermediates, or their removal. Here we review how this substrate promiscuity can account for the detrimental and beneficial impacts of RNA insertions during genome metabolism. We summarize how in vivo and in vitro experiments support the contribution of DNA polymerases and homologous recombination proteins in the formation of RNA-containing structures, and we discuss the role of DNA repair enzymes in their removal. The diversity of pathways that are thus affected by RNA insertions likely reflects the ancestral function of RNA molecules in genome maintenance and transmission.
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Affiliation(s)
- Benoit Palancade
- Institut Jacques Monod, Université de Paris, CNRS, F-75006 Paris, France
- Correspondence: (B.P.); (R.R.)
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Correspondence: (B.P.); (R.R.)
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24
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Senataxin Ortholog Sen1 Limits DNA:RNA Hybrid Accumulation at DNA Double-Strand Breaks to Control End Resection and Repair Fidelity. Cell Rep 2021; 31:107603. [PMID: 32375052 DOI: 10.1016/j.celrep.2020.107603] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/07/2020] [Accepted: 04/10/2020] [Indexed: 11/20/2022] Open
Abstract
An important but still enigmatic function of DNA:RNA hybrids is their role in DNA double-strand break (DSB) repair. Here, we show that Sen1, the budding yeast ortholog of the human helicase Senataxin, is recruited at an HO endonuclease-induced DSB and limits the local accumulation of DNA:RNA hybrids. In the absence of Sen1, hybrid accumulation proximal to the DSB promotes increased binding of the Ku70-80 (KU) complex at the break site, mutagenic non-homologous end joining (NHEJ), micro-homology-mediated end joining (MMEJ), and chromosome translocations. We also show that homology-directed recombination (HDR) by gene conversion is mostly proficient in sen1 mutants after single DSB. However, in the absence of Sen1, DNA:RNA hybrids, Mre11, and Dna2 initiate resection through a non-canonical mechanism. We propose that this resection mechanism through local DNA:RNA hybrids acts as a backup to prime HDR when canonical pathways are altered, but at the expense of genome integrity.
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25
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High Flexibility of RNaseH2 Catalytic Activity with Respect to Non-Canonical DNA Structures. Int J Mol Sci 2021; 22:ijms22105201. [PMID: 34068992 PMCID: PMC8155979 DOI: 10.3390/ijms22105201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2'-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA replication causing replicative fork stalling and collapse. Ribonucleotide removal is initiated by Ribonuclease H2 (RNase H2), the key player in Ribonucleotide Excision Repair (RER). Its absence leads to embryonic lethality in mice, while mutations decreasing its activity cause Aicardi-Goutières syndrome. DNA geometry can be altered by DNA lesions or by peculiar sequences forming secondary structures, like G-quadruplex (G4) and trinucleotide repeats (TNR) hairpins, which significantly differ from canonical B-form. Ribonucleotides pairing to lesioned nucleotides, or incorporated within non-B DNA structures could avoid RNase H2 recognition, potentially contributing to genome instability. In this work, we investigate the ability of RNase H2 to process misincorporated ribonucleotides in a panel of DNA substrates showing different geometrical features. RNase H2 proved to be a flexible enzyme, recognizing as a substrate the majority of the constructs we generated. However, some geometrical features and non-canonical DNA structures severely impaired its activity, suggesting a relevant role of misincorporated ribonucleotides in the physiological instability of specific DNA sequences.
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26
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Ashour ME, Mosammaparast N. Mechanisms of damage tolerance and repair during DNA replication. Nucleic Acids Res 2021; 49:3033-3047. [PMID: 33693881 PMCID: PMC8034635 DOI: 10.1093/nar/gkab101] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/28/2021] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Accurate duplication of chromosomal DNA is essential for the transmission of genetic information. The DNA replication fork encounters template lesions, physical barriers, transcriptional machinery, and topological barriers that challenge the faithful completion of the replication process. The flexibility of replisomes coupled with tolerance and repair mechanisms counteract these replication fork obstacles. The cell possesses several universal mechanisms that may be activated in response to various replication fork impediments, but it has also evolved ways to counter specific obstacles. In this review, we will discuss these general and specific strategies to counteract different forms of replication associated damage to maintain genomic stability.
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Affiliation(s)
- Mohamed Elsaid Ashour
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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27
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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28
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Zhou ZX, Williams JS, Lujan SA, Kunkel TA. Ribonucleotide incorporation into DNA during DNA replication and its consequences. Crit Rev Biochem Mol Biol 2021; 56:109-124. [PMID: 33461360 DOI: 10.1080/10409238.2020.1869175] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Ribonucleotides are the most abundant non-canonical nucleotides in the genome. Their vast presence and influence over genome biology is becoming increasingly appreciated. Here we review the recent progress made in understanding their genomic presence, incorporation characteristics and usefulness as biomarkers for polymerase enzymology. We also discuss ribonucleotide processing, the genetic consequences of unrepaired ribonucleotides in DNA and evidence supporting the significance of their transient presence in the nuclear genome.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Jessica S Williams
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Scott A Lujan
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Thomas A Kunkel
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
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29
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Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
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Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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30
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Meers C, Keskin H, Banyai G, Mazina O, Yang T, Gombolay AL, Mukherjee K, Kaparos EI, Newnam G, Mazin A, Storici F. Genetic Characterization of Three Distinct Mechanisms Supporting RNA-Driven DNA Repair and Modification Reveals Major Role of DNA Polymerase ζ. Mol Cell 2020; 79:1037-1050.e5. [PMID: 32882183 DOI: 10.1016/j.molcel.2020.08.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/30/2020] [Accepted: 08/12/2020] [Indexed: 01/08/2023]
Abstract
DNA double-stranded breaks (DSBs) are dangerous lesions threatening genomic stability. Fidelity of DSB repair is best achieved by recombination with a homologous template sequence. In yeast, transcript RNA was shown to template DSB repair of DNA. However, molecular pathways of RNA-driven repair processes remain obscure. Utilizing assays of RNA-DNA recombination with and without an induced DSB in yeast DNA, we characterize three forms of RNA-mediated genomic modifications: RNA- and cDNA-templated DSB repair (R-TDR and c-TDR) using an RNA transcript or a DNA copy of the RNA transcript for DSB repair, respectively, and a new mechanism of RNA-templated DNA modification (R-TDM) induced by spontaneous or mutagen-induced breaks. While c-TDR requires reverse transcriptase, translesion DNA polymerase ζ (Pol ζ) plays a major role in R-TDR, and it is essential for R-TDM. This study characterizes mechanisms of RNA-DNA recombination, uncovering a role of Pol ζ in transferring genetic information from transcript RNA to DNA.
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Affiliation(s)
- Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Havva Keskin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gabor Banyai
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olga Mazina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Efiyenia I Kaparos
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexander Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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31
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32
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Wang F, Li P, Shao Y, Li Y, Zhang K, Li M, Wang R, Zheng S, Wang Y, Song S, Feng S, Liu F, Xiao W, Li X. Site-specific proteolytic cleavage prevents ubiquitination and degradation of human REV3L, the catalytic subunit of DNA polymerase ζ. Nucleic Acids Res 2020; 48:3619-3637. [PMID: 32064513 PMCID: PMC7144948 DOI: 10.1093/nar/gkaa096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 01/18/2023] Open
Abstract
REV3L, the catalytic subunit of DNA polymerase ζ (Pol ζ), is indispensable for translesion DNA synthesis, which protects cells from deleterious DNA lesions resulting from various intrinsic and environmental sources. However, REV3L lacks a proofreading exonuclease activity and consequently bypasses DNA lesions at the expense of increased mutations, which poses a severe threat to genome stability. Here we report a site-specific proteolytic event of human REV3L. We show that REV3L is cleaved by a threonine aspartase, Taspase1 (TASP1), to generate an N-terminal 70-kDa fragment (N70) and a polypeptide carrying the C-terminal polymerase catalytic domain in human cells. Strikingly, such a post-translational cleavage event plays a vital role in controlling REV3L stability by preventing ubiquitination and proteasome-mediated degradation of REV3L. Indicative of the biological importance of the above REV3L post-translational processing, cellular responses to UV and cisplatin-induced DNA lesions are markedly impaired in human HCT116 cell derivatives bearing defined point mutations in the endogenous REV3L gene that compromise REV3L cleavage. These findings establish a new paradigm in modulating the abundance of REV3L through site-specific proteolysis in human cells.
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Affiliation(s)
- Fengting Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Pan Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuan Shao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yanyan Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Kai Zhang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Miaomiao Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Rong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shuo Zheng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yingying Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Sen Song
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shiguo Feng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Fei Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Xialu Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
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33
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Masłowska KH, Laureti L, Pagès V. iDamage: a method to integrate modified DNA into the yeast genome. Nucleic Acids Res 2020; 47:e124. [PMID: 31418026 PMCID: PMC6846816 DOI: 10.1093/nar/gkz723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022] Open
Abstract
In order to explore the mechanisms employed by living cells to deal with DNA alterations, we have developed a method by which we insert a modified DNA into a specific site of the yeast genome. This is achieved by the site-specific integration of a modified plasmid at a chosen locus of the genome of Saccharomyces cerevisiae, through the use of the Cre/lox recombination system. In the present work, we have used our method to insert a single UV lesion into the yeast genome, and studied how the balance between error-free and error-prone lesion bypass is regulated. We show that the inhibition of homologous recombination, either directly (by the inactivation of Rad51 recombinase) or through its control by preventing the polyubiquitination of PCNA (ubc13 mutant), leads to a strong increase in the use of Trans Lesion Synthesis (TLS). Such regulatory aspects of DNA damage tolerance could not have been observed with previous strategies using plasmid or randomly distributed DNA lesions, which shows the advantage of our new method. The very robust and precise integration of any modified DNA at any chosen locus of the yeast genome that we describe here is a powerful tool that will enable the exploration of many biological processes related to replication and repair of modified DNA.
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Affiliation(s)
- Katarzyna H Masłowska
- CRCM: Team DNA Damage and Genome Instability
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Luisa Laureti
- CRCM: Team DNA Damage and Genome Instability
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Vincent Pagès
- CRCM: Team DNA Damage and Genome Instability
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, Marseille, France
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34
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Basbous J, Aze A, Chaloin L, Lebdy R, Hodroj D, Ribeyre C, Larroque M, Shepard C, Kim B, Pruvost A, Moreaux J, Maiorano D, Mechali M, Constantinou A. Dihydropyrimidinase protects from DNA replication stress caused by cytotoxic metabolites. Nucleic Acids Res 2020; 48:1886-1904. [PMID: 31853544 PMCID: PMC7038975 DOI: 10.1093/nar/gkz1162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/28/2023] Open
Abstract
Imbalance in the level of the pyrimidine degradation products dihydrouracil and dihydrothymine is associated with cellular transformation and cancer progression. Dihydropyrimidines are degraded by dihydropyrimidinase (DHP), a zinc metalloenzyme that is upregulated in solid tumors but not in the corresponding normal tissues. How dihydropyrimidine metabolites affect cellular phenotypes remains elusive. Here we show that the accumulation of dihydropyrimidines induces the formation of DNA-protein crosslinks (DPCs) and causes DNA replication and transcriptional stress. We used Xenopus egg extracts to recapitulate DNA replication invitro. We found that dihydropyrimidines interfere directly with the replication of both plasmid and chromosomal DNA. Furthermore, we show that the plant flavonoid dihydromyricetin inhibits human DHP activity. Cellular exposure to dihydromyricetin triggered DPCs-dependent DNA replication stress in cancer cells. This study defines dihydropyrimidines as potentially cytotoxic metabolites that may offer an opportunity for therapeutic-targeting of DHP activity in solid tumors.
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Affiliation(s)
- Jihane Basbous
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Antoine Aze
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, 34293 Montpellier Cedex 5, France
| | - Rana Lebdy
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Dana Hodroj
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France.,Cancer Research Center of Toulouse (CRCT), 31037 Toulouse Cedex 1, France
| | - Cyril Ribeyre
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Marion Larroque
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France.,Institut du Cancer de Montpellier (ICM),34298 Montpellier Cedex 5, France
| | - Caitlin Shepard
- School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Baek Kim
- School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Alain Pruvost
- Service de Pharmacologie et Immunoanalyse (SPI), Plateforme SMArt-MS, CEA, INRA, Université Paris-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Jérôme Moreaux
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Domenico Maiorano
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Marcel Mechali
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Angelos Constantinou
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
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35
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Nava GM, Grasso L, Sertic S, Pellicioli A, Muzi Falconi M, Lazzaro F. One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA. Int J Mol Sci 2020; 21:E1706. [PMID: 32131532 PMCID: PMC7084774 DOI: 10.3390/ijms21051706] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
In the last decade, it has become evident that RNA is frequently found in DNA. It is now well established that single embedded ribonucleoside monophosphates (rNMPs) are primarily introduced by DNA polymerases and that longer stretches of RNA can anneal to DNA, generating RNA:DNA hybrids. Among them, the most studied are R-loops, peculiar three-stranded nucleic acid structures formed upon the re-hybridization of a transcript to its template DNA. In addition, polyribonucleotide chains are synthesized to allow DNA replication priming, double-strand breaks repair, and may as well result from the direct incorporation of consecutive rNMPs by DNA polymerases. The bright side of RNA into DNA is that it contributes to regulating different physiological functions. The dark side, however, is that persistent RNA compromises genome integrity and genome stability. For these reasons, the characterization of all these structures has been under growing investigation. In this review, we discussed the origin of single and multiple ribonucleotides in the genome and in the DNA of organelles, focusing on situations where the aberrant processing of RNA:DNA hybrids may result in multiple rNMPs embedded in DNA. We concluded by providing an overview of the currently available strategies to study the presence of single and multiple ribonucleotides in DNA in vivo.
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Affiliation(s)
| | | | | | | | - Marco Muzi Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
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36
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Kellner V, Luke B. Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair. EMBO J 2020; 39:e102309. [PMID: 31833079 PMCID: PMC6996501 DOI: 10.15252/embj.2019102309] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/22/2019] [Accepted: 11/26/2019] [Indexed: 01/11/2023] Open
Abstract
The duplication of the eukaryotic genome is an intricate process that has to be tightly safe-guarded. One of the most frequently occurring errors during DNA synthesis is the mis-insertion of a ribonucleotide instead of a deoxyribonucleotide. Ribonucleotide excision repair (RER) is initiated by RNase H2 and results in error-free removal of such mis-incorporated ribonucleotides. If left unrepaired, DNA-embedded ribonucleotides result in a variety of alterations within chromosomal DNA, which ultimately lead to genome instability. Here, we review how genomic ribonucleotides lead to chromosomal aberrations and discuss how the tight regulation of RER timing may be important for preventing unwanted DNA damage. We describe the structural impact of unrepaired ribonucleotides on DNA and chromatin and comment on the potential consequences for cellular fitness. In the context of the molecular mechanisms associated with faulty RER, we have placed an emphasis on how and why increased levels of genomic ribonucleotides are associated with severe autoimmune syndromes, neuropathology, and cancer. In addition, we discuss therapeutic directions that could be followed for pathologies associated with defective removal of ribonucleotides from double-stranded DNA.
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Affiliation(s)
- Vanessa Kellner
- Institute of Molecular Biology (IMB)MainzGermany
- Present address:
Department of BiologyNew York UniversityNew YorkNYUSA
| | - Brian Luke
- Institute of Molecular Biology (IMB)MainzGermany
- Institute of Developmental Biology and Neurobiology (IDN)Johannes Gutenberg UniversitätMainzGermany
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37
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Martin SK, Wood RD. DNA polymerase ζ in DNA replication and repair. Nucleic Acids Res 2019; 47:8348-8361. [PMID: 31410467 PMCID: PMC6895278 DOI: 10.1093/nar/gkz705] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022] Open
Abstract
Here, we survey the diverse functions of DNA polymerase ζ (pol ζ) in eukaryotes. In mammalian cells, REV3L (3130 residues) is the largest catalytic subunit of the DNA polymerases. The orthologous subunit in yeast is Rev3p. Pol ζ also includes REV7 subunits (encoded by Rev7 in yeast and MAD2L2 in mammalian cells) and two subunits shared with the replicative DNA polymerase, pol δ. Pol ζ is used in response to circumstances that stall DNA replication forks in both yeast and mammalian cells. The best-examined situation is translesion synthesis at sites of covalent DNA lesions such as UV radiation-induced photoproducts. We also highlight recent evidence that uncovers various roles of pol ζ that extend beyond translesion synthesis. For instance, pol ζ is also employed when the replisome operates sub-optimally or at difficult-to-replicate DNA sequences. Pol ζ also participates in repair by microhomology mediated break-induced replication. A rev3 deletion is tolerated in yeast but Rev3l disruption results in embryonic lethality in mice. Inactivation of mammalian Rev3l results in genomic instability and invokes cell death and senescence programs. Targeting of pol ζ function may be a useful strategy in cancer therapy, although chromosomal instability associated with pol ζ deficiency must be considered.
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Affiliation(s)
- Sara K Martin
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA and The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA and The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences
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38
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Xie Y, Wang N, Li Y, Deng T, Li J, Zhang K, Yu R. Cyclodextrin supramolecular inclusion-enhanced pyrene excimer switching for highly selective detection of RNase H. Anal Chim Acta 2019; 1088:137-143. [PMID: 31623709 DOI: 10.1016/j.aca.2019.08.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/13/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022]
Abstract
Here, we report a novel fluorescence method for the highly selective and sensitive detection of RNase H by combining the use of a dual-pyrene-labeled DNA/RNA duplex with supramolecular inclusion-enhanced fluorescence. Initially, the probe is in the "off" state due to the rigidness of the double-stranded duplex, which separates the two pyrene units. In the presence of RNase H, the RNA strand of the DNA/RNA duplex will be hydrolyzed, and the DNA strand transforms into a hairpin structure, bringing close the two pyrene units which in turn enter the hydrophobic cavity of a γ-cyclodextrin. As a result, the pyrene excimer emission is greatly enhanced, thereby realizing the detection of RNase H activity. Under optimal conditions, RNase H detection can be achieved in the range from 0.08 to 4 U/mL, with a detection limit of 0.02 U/mL.
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Affiliation(s)
- Ye Xie
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ningning Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yulong Li
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ting Deng
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Ke Zhang
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Ruqin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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Pilzecker B, Buoninfante OA, Jacobs H. DNA damage tolerance in stem cells, ageing, mutagenesis, disease and cancer therapy. Nucleic Acids Res 2019; 47:7163-7181. [PMID: 31251805 PMCID: PMC6698745 DOI: 10.1093/nar/gkz531] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA damage response network guards the stability of the genome from a plethora of exogenous and endogenous insults. An essential feature of the DNA damage response network is its capacity to tolerate DNA damage and structural impediments during DNA synthesis. This capacity, referred to as DNA damage tolerance (DDT), contributes to replication fork progression and stability in the presence of blocking structures or DNA lesions. Defective DDT can lead to a prolonged fork arrest and eventually cumulate in a fork collapse that involves the formation of DNA double strand breaks. Four principal modes of DDT have been distinguished: translesion synthesis, fork reversal, template switching and repriming. All DDT modes warrant continuation of replication through bypassing the fork stalling impediment or repriming downstream of the impediment in combination with filling of the single-stranded DNA gaps. In this way, DDT prevents secondary DNA damage and critically contributes to genome stability and cellular fitness. DDT plays a key role in mutagenesis, stem cell maintenance, ageing and the prevention of cancer. This review provides an overview of the role of DDT in these aspects.
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Affiliation(s)
- Bas Pilzecker
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Olimpia Alessandra Buoninfante
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Cerritelli SM, Crouch RJ. RNase H2-RED carpets the path to eukaryotic RNase H2 functions. DNA Repair (Amst) 2019; 84:102736. [PMID: 31761672 PMCID: PMC6936605 DOI: 10.1016/j.dnarep.2019.102736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022]
Abstract
Eukaryotic RNases H2 have dual functions in initiating the removal of ribonucleoside monophosphates (rNMPs) incorporated by DNA polymerases during DNA synthesis and in cleaving the RNA moiety of RNA/DNA hybrids formed during transcription and retrotransposition. The other major cellular RNase H, RNase H1, shares the hybrid processing activity, but not all substrates. After RNase H2 incision at the rNMPs in DNA the Ribonucleotide Excision Repair (RER) pathway completes the removal, restoring dsDNA. The development of the RNase H2-RED (Ribonucleotide Excision Defective) mutant enzyme, which can process RNA/DNA hybrids but is unable to cleave rNMPs embedded in DNA has unlinked the two activities and illuminated the roles of RNase H2 in cellular metabolism. Studies mostly in Saccharomyces cerevisiae, have shown both activities of RNase H2 are necessary to maintain genome integrity and that RNase H1 and H2 have overlapping as well as distinct RNA/DNA hybrid substrates. In mouse RNase H2-RED confirmed that rNMPs in DNA during embryogenesis induce lethality in a p53-dependent DNA damage response. In mammalian cell cultures, RNase H2-RED helped identifying DNA lesions produced by Top1 cleavage at rNMPs and led to determine that RNase H2 participates in the retrotransposition of LINE-1 elements. In this review, we summarize the studies and conclusions reached by utilization of RNase H2-RED enzyme in different model systems.
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Affiliation(s)
- Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Lockhart A, Pires VB, Bento F, Kellner V, Luke-Glaser S, Yakoub G, Ulrich HD, Luke B. RNase H1 and H2 Are Differentially Regulated to Process RNA-DNA Hybrids. Cell Rep 2019; 29:2890-2900.e5. [DOI: 10.1016/j.celrep.2019.10.108] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/10/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022] Open
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42
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Walsh E, Henrikus SS, Vaisman A, Makiela-Dzbenska K, Armstrong TJ, Łazowski K, McDonald JP, Goodman MF, van Oijen AM, Jonczyk P, Fijalkowska IJ, Robinson A, Woodgate R. Role of RNase H enzymes in maintaining genome stability in Escherichia coli expressing a steric-gate mutant of pol V ICE391. DNA Repair (Amst) 2019; 84:102685. [PMID: 31543434 DOI: 10.1016/j.dnarep.2019.102685] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/18/2022]
Abstract
pol VICE391 (RumA'2B) is a low-fidelity polymerase that promotes considerably higher levels of spontaneous "SOS-induced" mutagenesis than the related E. coli pol V (UmuD'2C). The molecular basis for the enhanced mutagenesis was previously unknown. Using single molecule fluorescence microscopy to visualize pol V enzymes, we discovered that the elevated levels of mutagenesis are likely due, in part, to prolonged binding of RumB to genomic DNA leading to increased levels of DNA synthesis compared to UmuC. We have generated a steric gate pol VICE391 variant (pol VICE391_Y13A) that readily misincorporates ribonucleotides into the E. coli genome and have used the enzyme to investigate the molecular mechanisms of Ribonucleotide Excision Repair (RER) under conditions of increased ribonucleotide-induced stress. To do so, we compared the extent of spontaneous mutagenesis promoted by pol V and pol VICE391 to that of their respective steric gate variants. Levels of mutagenesis promoted by the steric gate variants that are lower than that of the wild-type enzyme are indicative of active RER that removes misincorporated ribonucleotides, but also misincorporated deoxyribonucleotides from the genome. Using such an approach, we confirmed that RNase HII plays a pivotal role in RER. In the absence of RNase HII, Nucleotide Excision Repair (NER) proteins help remove misincorporated ribonucleotides. However, significant RER occurs in the absence of RNase HII and NER. Most of the RNase HII and NER-independent RER occurs on the lagging strand during genome duplication. We suggest that this is most likely due to efficient RNase HI-dependent RER which recognizes the polyribonucleotide tracts generated by pol VICE391_Y13A. These activities are critical for the maintenance of genomic integrity when RNase HII is overwhelmed, or inactivated, as ΔrnhB or ΔrnhB ΔuvrA strains expressing pol VICE391_Y13A exhibit genome and plasmid instability in the absence of RNase HI.
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Affiliation(s)
- Erin Walsh
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Sarah S Henrikus
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | | | - Thomas J Armstrong
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Krystian Łazowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910 USA
| | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA.
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Williams JS, Lujan SA, Zhou ZX, Burkholder AB, Clark AB, Fargo DC, Kunkel TA. Genome-wide mutagenesis resulting from topoisomerase 1-processing of unrepaired ribonucleotides in DNA. DNA Repair (Amst) 2019; 84:102641. [PMID: 31311768 DOI: 10.1016/j.dnarep.2019.102641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 01/10/2023]
Abstract
Ribonucleotides are the most common non-canonical nucleotides incorporated into DNA during replication, and their processing leads to mutations and genome instability. Yeast mutation reporter systems demonstrate that 2-5 base pair deletions (Δ2-5bp) in repetitive DNA are a signature of unrepaired ribonucleotides, and that these events are initiated by topoisomerase 1 (Top1) cleavage. However, a detailed understanding of the frequency and locations of ribonucleotide-dependent mutational events across the genome has been lacking. Here we present the results of genome-wide mutational analysis of yeast strains deficient in Ribonucleotide Excision Repair (RER). We identified mutations that accumulated over thousands of generations in strains expressing either wild-type or variant replicase alleles (M644G Pol ε, L612M Pol δ, L868M Pol α) that confer increased ribonucleotide incorporation into DNA. Using a custom-designed mutation-calling pipeline called muver (for mutationes verificatae), we observe a number of surprising mutagenic features. This includes a 24-fold preferential elevation of AG and AC relative to AT dinucleotide deletions in the absence of RER, suggesting specificity for Top1-initiated deletion mutagenesis. Moreover, deletion rates in di- and trinucleotide repeat tracts increase exponentially with tract length. Consistent with biochemical and reporter gene mutational analysis, these deletions are no longer observed upon deletion of TOP1. Taken together, results from these analyses demonstrate the global impact of genomic ribonucleotide processing by Top1 on genome integrity.
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Affiliation(s)
- Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Zhi-Xiong Zhou
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Adam B Burkholder
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Alan B Clark
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - David C Fargo
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA.
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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45
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Gallo D, Brown GW. Post-replication repair: Rad5/HLTF regulation, activity on undamaged templates, and relationship to cancer. Crit Rev Biochem Mol Biol 2019; 54:301-332. [PMID: 31429594 DOI: 10.1080/10409238.2019.1651817] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/12/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022]
Abstract
The eukaryotic post-replication repair (PRR) pathway allows completion of DNA replication when replication forks encounter lesions on the DNA template and are mediated by post-translational ubiquitination of the DNA sliding clamp proliferating cell nuclear antigen (PCNA). Monoubiquitinated PCNA recruits translesion synthesis (TLS) polymerases to replicate past DNA lesions in an error-prone manner while addition of K63-linked polyubiquitin chains signals for error-free template switching to the sister chromatid. Central to both branches is the E3 ubiquitin ligase and DNA helicase Rad5/helicase-like transcription factor (HLTF). Mutations in PRR pathway components lead to genomic rearrangements, cancer predisposition, and cancer progression. Recent studies have challenged the notion that the PRR pathway is involved only in DNA lesion tolerance and have shed new light on its roles in cancer progression. Molecular details of Rad5/HLTF recruitment and function at replication forks have emerged. Mounting evidence indicates that PRR is required during lesion-less replication stress, leading to TLS polymerase activity on undamaged templates. Analysis of PRR mutation status in human cancers and PRR function in cancer models indicates that down regulation of PRR activity is a viable strategy to inhibit cancer cell growth and reduce chemoresistance. Here, we review these findings, discuss how they change our views of current PRR models, and look forward to targeting the PRR pathway in the clinic.
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Affiliation(s)
- David Gallo
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
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46
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Zhou Y, Zhang J, Jiang Q, Lu J. An allosteric switch-based hairpin for label-free chemiluminescence detection of ribonuclease H activity and inhibitors. Analyst 2019; 144:1420-1425. [PMID: 30607414 DOI: 10.1039/c8an02006j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To assay enzyme activities and screen its inhibitors, we demonstrated a novel label-free chemiluminescent (CL) aptasensor for the sensitive detection of RNase H activity based on hairpin technology. The specific hairpin structure was a DNA-RNA chimeric strand, which contained a streptavidin aptamer sequence and a blocked RNA sequence. RNase H could specifically recognize and cleave the RNA sequence of the DNA-RNA hybrid stem, liberating the streptavidin aptamer which could be accumulated by streptavidin-coated magnetic microspheres (SA-MP). Then the CL signal was generated due to an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxyphenyl-glyoxal (TMPG) and the guanine (G) nucleotides in the SA aptamer. This novel assay method exhibited a good linear relationship in the range of 0.1-10 U mL-1 under the optimized conditions. Our results suggested that the developed system was a promising platform for monitoring the RNase H activity and showed great potential in biomedical studies and drug screening.
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Affiliation(s)
- Ying Zhou
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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47
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Meroni A, Nava GM, Bianco E, Grasso L, Galati E, Bosio MC, Delmastro D, Muzi-Falconi M, Lazzaro F. RNase H activities counteract a toxic effect of Polymerase η in cells replicating with depleted dNTP pools. Nucleic Acids Res 2019; 47:4612-4623. [PMID: 30847483 PMCID: PMC6511917 DOI: 10.1093/nar/gkz165] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 02/25/2019] [Accepted: 03/01/2019] [Indexed: 01/27/2023] Open
Abstract
RNA:DNA hybrids are transient physiological intermediates that arise during several cellular processes such as DNA replication. In pathological situations, they may stably accumulate and pose a threat to genome integrity. Cellular RNase H activities process these structures to restore the correct DNA:DNA sequence. Yeast cells lacking RNase H are negatively affected by depletion of deoxyribonucleotide pools necessary for DNA replication. Here we show that the translesion synthesis DNA polymerase η (Pol η) plays a role in DNA replication under low deoxyribonucleotides condition triggered by hydroxyurea. In particular, the catalytic reaction performed by Pol η is detrimental for RNase H deficient cells, causing DNA damage checkpoint activation and G2/M arrest. Moreover, a Pol η mutant allele with enhanced ribonucleotide incorporation further exacerbates the sensitivity to hydroxyurea of cells lacking RNase H activities. Our data are compatible with a model in which Pol η activity facilitates the formation or stabilization of RNA:DNA hybrids at stalled replication forks. However, in a scenario where RNase H activity fails to restore DNA, these hybrids become highly toxic for cells.
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Affiliation(s)
- Alice Meroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Giulia Maria Nava
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Eliana Bianco
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Lavinia Grasso
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Elena Galati
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Maria Cristina Bosio
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Daria Delmastro
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
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48
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Qiu Z, Zhu L, He L, Chen D, Zeng D, Chen G, Hu J, Zhang G, Ren D, Dong G, Gao Z, Shen L, Zhang Q, Guo L, Qian Q. DNA damage and reactive oxygen species cause cell death in the rice local lesions 1 mutant under high light and high temperature. THE NEW PHYTOLOGIST 2019; 222:349-365. [PMID: 30449034 DOI: 10.1111/nph.15597] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/07/2018] [Indexed: 05/17/2023]
Abstract
High light and high temperature (HLHT) stress may become more frequent and severe as the climate changes, affecting crop growth and resulting in reduced production. However, the mechanism of the response to HLHT stress in rice is not yet fully understood. In the present study, we screened a rice mutant library using HLHT conditions and isolated an HLHT-sensitive mutant, local lesions 1 (ls1), which showed decreased pigment contents, defective stomata and chloroplasts, and a local lesions phenotype under HLHT. We characterized and cloned LS1 by map-based cloning and genetic complementation. LS1 encodes the A subunit of the RNase H2 complex (RNASEH2A). Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) and comet assays indicated that mutation of LS1 led to severe DNA damage under HLHT stress. Furthermore, we found excessive reactive oxygen species (ROS) accumulation in the ls1 mutant under HLHT stress. Exogenous antioxidants eased the local lesions phenotype of the ls1 mutant under HLHT. DNA damage caused by HLHT stress induces ROS accumulation, which causes the injury and apoptosis of leaf cells in the ls1 mutant. These results enhance our understanding of the regulatory mechanism in the response to HLHT stress in higher plants.
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Affiliation(s)
- Zhennan Qiu
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Lei He
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Dongdong Chen
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
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Su Y, Ghodke PP, Egli M, Li L, Wang Y, Guengerich FP. Human DNA polymerase η has reverse transcriptase activity in cellular environments. J Biol Chem 2019; 294:6073-6081. [PMID: 30842261 DOI: 10.1074/jbc.ra119.007925] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Indexed: 12/24/2022] Open
Abstract
Classical DNA and RNA polymerase (pol) enzymes have defined roles with their respective substrates, but several pols have been found to have multiple functions. We reported previously that purified human DNA pol η (hpol η) can incorporate both deoxyribonucleoside triphosphates (dNTPs) and ribonucleoside triphosphates (rNTPs) and can use both DNA and RNA as substrates. X-ray crystal structures revealed that two pol η residues, Phe-18 and Tyr-92, behave as steric gates to influence sugar selectivity. However, the physiological relevance of these phenomena has not been established. Here, we show that purified hpol η adds rNTPs to DNA primers at physiological rNTP concentrations and in the presence of competing dNTPs. When two rATPs were inserted opposite a cyclobutane pyrimidine dimer, the substrate was less efficiently cleaved by human RNase H2. Human XP-V fibroblast extracts, devoid of hpol η, could not add rNTPs to a DNA primer, but the expression of transfected hpol η in the cells restored this ability. XP-V cell extracts did not add dNTPs to DNA primers hybridized to RNA, but could when hpol η was expressed in the cells. HEK293T cell extracts could add dNTPs to DNA primers hybridized to RNA, but lost this ability if hpol η was deleted. Interestingly, a similar phenomenon was not observed when other translesion synthesis (TLS) DNA polymerases-hpol ι, κ, or ζ-were individually deleted. These results suggest that hpol η is one of the major reverse transcriptases involved in physiological processes in human cells.
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Affiliation(s)
- Yan Su
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Pratibha P Ghodke
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Martin Egli
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Lin Li
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
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50
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Makharashvili N, Arora S, Yin Y, Fu Q, Wen X, Lee JH, Kao CH, Leung JWC, Miller KM, Paull TT. Sae2/CtIP prevents R-loop accumulation in eukaryotic cells. eLife 2018; 7:e42733. [PMID: 30523780 PMCID: PMC6296784 DOI: 10.7554/elife.42733] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023] Open
Abstract
The Sae2/CtIP protein is required for efficient processing of DNA double-strand breaks that initiate homologous recombination in eukaryotic cells. Sae2/CtIP is also important for survival of single-stranded Top1-induced lesions and CtIP is known to associate directly with transcription-associated complexes in mammalian cells. Here we investigate the role of Sae2/CtIP at single-strand lesions in budding yeast and in human cells and find that depletion of Sae2/CtIP promotes the accumulation of stalled RNA polymerase and RNA-DNA hybrids at sites of highly expressed genes. Overexpression of the RNA-DNA helicase Senataxin suppresses DNA damage sensitivity and R-loop accumulation in Sae2/CtIP-deficient cells, and a catalytic mutant of CtIP fails to complement this sensitivity, indicating a role for CtIP nuclease activity in the repair process. Based on this evidence, we propose that R-loop processing by 5' flap endonucleases is a necessary step in the stabilization and removal of nascent R-loop initiating structures in eukaryotic cells.
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Affiliation(s)
- Nodar Makharashvili
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Sucheta Arora
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Yizhi Yin
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Qiong Fu
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Xuemei Wen
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Ji-Hoon Lee
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Chung-Hsuan Kao
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Justin WC Leung
- Department of Radiation OncologyUniversity of Arkansas for Medical SciencesLittle RockUnited States
| | - Kyle M Miller
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Tanya T Paull
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
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