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Corazzi L, Ionasz VS, Andrejev S, Wang LC, Vouzas A, Giaisi M, Di Muzio G, Ding B, Marx AJM, Henkenjohann J, Allers MM, Gilbert DM, Wei PC. Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters. Nat Commun 2024; 15:3594. [PMID: 38678011 PMCID: PMC11055891 DOI: 10.1038/s41467-024-47934-w] [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: 08/22/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Recurrent DNA break clusters (RDCs) are replication-transcription collision hotspots; many are unique to neural progenitor cells. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unravel the replication features dictating RDC location and orientation. Most RDCs occur at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSBs), while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bound RNA reveals co-transcriptional dual-strand DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping RNA polymerase activity uncovers that head-to-head interactions between replication and transcription machinery result in 60% DSB contribution to the head-on compared to 40% for co-directional. Taken together we reveal TTR as a fragile class and show how the linear interaction between transcription and replication impacts genome stability.
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Affiliation(s)
- Lorenzo Corazzi
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Vivien S Ionasz
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Li-Chin Wang
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Athanasios Vouzas
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Marco Giaisi
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Giulia Di Muzio
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Boyu Ding
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Faculty of Medicine, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Anna J M Marx
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Jonas Henkenjohann
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Michael M Allers
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Medicine, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Pei-Chi Wei
- German Cancer Research Center, 69120, Heidelberg, Germany.
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany.
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany.
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2
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Corazzi L, Ionasz V, Andrejev S, Wang LC, Vouzas A, Giaisi M, Di Muzio G, Ding B, Marx AJM, Henkenjohann J, Allers MM, Gilbert DM, Wei PC. Linear Interaction Between Replication and Transcription Shapes DNA Break Dynamics at Recurrent DNA Break Clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554340. [PMID: 37662334 PMCID: PMC10473677 DOI: 10.1101/2023.08.22.554340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Recurrent DNA break clusters (RDCs) are replication-transcription collision hotspots; many are unique to neural progenitor cells. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unraveled the replication features dictating RDC location and orientation. Most RDCs occur at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSBs), while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bound RNA revealed co-transcriptional dual-strand DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping RNA polymerase activity revealed that head-to-head interactions between replication and transcription machinery resulted in 60% DSB contribution to the head-on compared to 40% for co-directional. Our findings revealed TTR as a novel fragile class and highlighted how the linear interaction between transcription and replication impacts genome stability.
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3
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Lee SY, Miller KM, Kim JJ. Clinical and Mechanistic Implications of R-Loops in Human Leukemias. Int J Mol Sci 2023; 24:ijms24065966. [PMID: 36983041 PMCID: PMC10052022 DOI: 10.3390/ijms24065966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic mutations or environmental agents are major contributors to leukemia and are associated with genomic instability. R-loops are three-stranded nucleic acid structures consisting of an RNA-DNA hybrid and a non-template single-stranded DNA. These structures regulate various cellular processes, including transcription, replication, and DSB repair. However, unregulated R-loop formation can cause DNA damage and genomic instability, which are potential drivers of cancer including leukemia. In this review, we discuss the current understanding of aberrant R-loop formation and how it influences genomic instability and leukemia development. We also consider the possibility of R-loops as therapeutic targets for cancer treatment.
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Affiliation(s)
- Seo-Yun Lee
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jae-Jin Kim
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
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4
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Pareek M, Hegedüs B, Hou Z, Csernetics Á, Wu H, Virágh M, Sahu N, Liu XB, Nagy L. Preassembled Cas9 Ribonucleoprotein-Mediated Gene Deletion Identifies the Carbon Catabolite Repressor and Its Target Genes in Coprinopsis cinerea. Appl Environ Microbiol 2022; 88:e0094022. [PMID: 36374019 PMCID: PMC9746306 DOI: 10.1128/aem.00940-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. The cre1 gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota species remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. We used a rapid and efficient gene deletion approach based on PCR-amplified split-marker DNA cassettes together with in vitro assembled Cas9-guide RNA ribonucleoproteins (Cas9 RNPs) to generate C. cinerea cre1 gene deletion strains. Gene expression profiling of two independent C. cinerea cre1 mutants showed significant deregulation of carbohydrate metabolism, plant cell wall degrading enzymes (PCWDEs), plasma membrane transporter-related and several transcription factor-encoding genes, among others. Our results support the notion that, like reports in the ascomycetes, Cre1 of C. cinerea orchestrates CCR through a combined regulation of diverse genes, including PCWDEs, transcription factors that positively regulate PCWDEs, and membrane transporters which could import simple sugars that can induce the expression of PWCDEs. Somewhat paradoxically, though in accordance with other Agaricomycetes, genes related to lignin degradation were mostly downregulated in cre1 mutants, indicating they fall under different regulation than other PCWDEs. The gene deletion approach and the data presented here will expand our knowledge of CCR in the Basidiomycota and provide functional hypotheses on genes related to plant biomass degradation. IMPORTANCE Mushroom-forming fungi include some of the most efficient lignocellulosic plant biomass degraders. They degrade dead plant materials by a battery of lignin-, cellulose-, hemicellulose-, and pectin-degrading enzymes, the encoding genes of which are under tight transcriptional control. One of the highest-level regulations of these metabolic enzymes is known as carbon catabolite repression, which is orchestrated by the transcription factor Cre1, and ensures that costly lignocellulose-degrading enzyme genes are expressed only when simple carbon sources (e.g., glucose) are not available. Here, we identified the Cre1 ortholog in a litter decomposer Agaricomycete, Coprinopsis cinerea, knocked it out, and characterized transcriptional changes in the mutants. We identified several dozen lignocellulolytic enzyme genes as well as membrane transporters and other transcription factors as putative target genes of C. cinerea cre1. These results extend knowledge on carbon catabolite repression to litter decomposer Basidiomycota.
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Affiliation(s)
- Manish Pareek
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Botond Hegedüs
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Zhihao Hou
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Árpád Csernetics
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Hongli Wu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Máté Virágh
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Neha Sahu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - László Nagy
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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Petermann E, Lan L, Zou L. Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat Rev Mol Cell Biol 2022; 23:521-540. [PMID: 35459910 DOI: 10.1038/s41580-022-00474-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
RNA-DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA-DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating gene expression and chromatin structure, but they also pose a threat to genomic stability, especially during DNA replication. To keep the genome stable, cells have evolved a slew of mechanisms to prevent aberrant R-loop accumulation. Although R-loops can cause DNA damage, they are also induced by DNA damage and act as key intermediates in DNA repair such as in transcription-coupled repair and RNA-templated DNA break repair. When the regulation of R-loops goes awry, pathological R-loops accumulate, which contributes to diseases such as neurodegeneration and cancer. In this Review, we discuss the current understanding of the sources of R-loops and RNA-DNA hybrids, mechanisms that suppress and resolve these structures, the impact of these structures on DNA repair and genome stability, and opportunities to therapeutically target pathological R-loops.
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Affiliation(s)
- Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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6
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Sobhy MA, Tehseen M, Takahashi M, Bralić A, De Biasio A, Hamdan SM. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Comput Struct Biotechnol J 2021; 19:4456-4471. [PMID: 34471492 PMCID: PMC8385120 DOI: 10.1016/j.csbj.2021.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an important component of the intricate molecular machinery for DNA replication and repair. FEN1 is a structure-specific 5' nuclease that cleaves nascent single-stranded 5' flaps during the maturation of Okazaki fragments. Here, we review our research primarily applying single-molecule fluorescence to resolve important mechanistic aspects of human FEN1 enzymatic reaction. The methodology presented in this review is aimed as a guide for tackling other biomolecular enzymatic reactions by fluorescence enhancement, quenching, and FRET and their combinations. Using these methods, we followed in real-time the structures of the substrate and product and 5' flap cleavage during catalysis. We illustrate that FEN1 actively bends the substrate to verify its features and continues to mold it to induce a protein disorder-to-order transitioning that controls active site assembly. This mechanism suppresses off-target cleavage of non-cognate substrates and promotes their dissociation with an accuracy that was underestimated from bulk assays. We determined that product release in FEN1 after the 5' flap release occurs in two steps; a brief binding to the bent nicked-product followed by longer binding to the unbent nicked-product before dissociation. Based on our cryo-electron microscopy structure of the human lagging strand replicase bound to FEN1, we propose how this two-step product release mechanism may regulate the final steps during the maturation of Okazaki fragments.
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Affiliation(s)
- Mohamed A Sobhy
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Williams JS, Tumbale PP, Arana ME, Rana JA, Williams RS, Kunkel TA. High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication. Nat Commun 2021; 12:482. [PMID: 33473124 PMCID: PMC7817679 DOI: 10.1038/s41467-020-20800-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
DNA ligase 1 (LIG1, Cdc9 in yeast) finalizes eukaryotic nuclear DNA replication by sealing Okazaki fragments using DNA end-joining reactions that strongly discriminate against incorrectly paired DNA substrates. Whether intrinsic ligation fidelity contributes to the accuracy of replication of the nuclear genome is unknown. Here, we show that an engineered low-fidelity LIG1Cdc9 variant confers a novel mutator phenotype in yeast typified by the accumulation of single base insertion mutations in homonucleotide runs. The rate at which these additions are generated increases upon concomitant inactivation of DNA mismatch repair, or by inactivation of the Fen1Rad27 Okazaki fragment maturation (OFM) nuclease. Biochemical and structural data establish that LIG1Cdc9 normally avoids erroneous ligation of DNA polymerase slippage products, and this protection is compromised by mutation of a LIG1Cdc9 high-fidelity metal binding site. Collectively, our data indicate that high-fidelity DNA ligation is required to prevent insertion mutations, and that this may be particularly critical following strand displacement synthesis during the completion of OFM.
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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, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Percy P Tumbale
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Mercedes E Arana
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Julian A Rana
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, 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, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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Maestroni L, Audry J, Luciano P, Coulon S, Géli V, Corda Y. RPA and Pif1 cooperate to remove G-rich structures at both leading and lagging strand. Cell Stress 2020; 4:48-63. [PMID: 32190820 PMCID: PMC7063842 DOI: 10.15698/cst2020.03.214] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In Saccharomyces cerevisiae, the absence of Pif1 helicase induces the instability of G4-containing CEB1 minisatellite during leading strand but not lagging strand replication. We report that RPA and Pif1 cooperate to maintain CEB1 stability when the G4 forming strand is either on the leading or lagging strand templates. At the leading strand, RPA acts in the same pathway as Pif1 to maintain CEB1 stability. Consistent with this result, RPA co-precipitates with Pif1. This association between Pif1 and RPA is affected by the rfa1-D228Y mutation that lowers the affinity of RPA in particular for G-rich single-stranded DNA. At the lagging strand, in contrast to pif1Δ, the rfa1-D228Y mutation strongly increases the frequency of CEB1 rearrangements. We explain that Pif1 is dispensable at the lagging strand DNA by the ability of RPA by itself to prevent formation of stable G-rich secondary structures during lagging strand synthesis. Remarkably, overexpression of Pif1 rescues the instability of CEB1 at the lagging strand in the rfa1-D228Y mutant indicating that Pif1 can also act at the lagging strand. We show that the effects of the rfa1-D228Y (rpa1-D223Y in fission yeast) are conserved in Schizosaccharomyces pombe. Finally, we report that RNase H1 interacts in a DNA-dependent manner with RPA in budding yeast, however overexpression of RNase H1 does not rescue CEB1 instability observed in pif1Δ and rfa1-D228Y mutants. Collectively these results add new insights about the general role of RPA in preventing formation of DNA secondary structures and in coordinating the action of factors aimed at resolving them.
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Affiliation(s)
- Laetitia Maestroni
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Julien Audry
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Pierre Luciano
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Stéphane Coulon
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Vincent Géli
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Yves Corda
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
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Large-scale contractions of Friedreich's ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability. Proc Natl Acad Sci U S A 2020; 117:1628-1637. [PMID: 31911468 PMCID: PMC6983365 DOI: 10.1073/pnas.1913416117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Expansions of GAA repeats cause a severe hereditary neurodegenerative disease, Friedreich’s ataxia. In this study, we characterized the mechanisms of GAA repeat contractions in a yeast experimental system. These mechanisms might, in the long run, aid development of a therapy for this currently incurable disease. We show that GAA repeats contract during DNA replication, which can explain the high level of somatic instability of this repeat in patient tissues. We also provided evidence that a triple-stranded DNA structure is at the heart of GAA repeat instability. This discovery highlights the role of triplex DNA in genome instability and human disease. Friedreich’s ataxia (FRDA) is a human hereditary disease caused by the presence of expanded (GAA)n repeats in the first intron of the FXN gene [V. Campuzano et al., Science 271, 1423–1427 (1996)]. In somatic tissues of FRDA patients, (GAA)n repeat tracts are highly unstable, with contractions more common than expansions [R. Sharma et al., Hum. Mol. Genet. 11, 2175–2187 (2002)]. Here we describe an experimental system to characterize GAA repeat contractions in yeast and to conduct a genetic analysis of this process. We found that large-scale contraction is a one-step process, resulting in a median loss of ∼60 triplet repeats. Our genetic analysis revealed that contractions occur during DNA replication, rather than by various DNA repair pathways. Repeats contract in the course of lagging-strand synthesis: The processivity subunit of DNA polymerase δ, Pol32, and the catalytic domain of Rev1, a translesion polymerase, act together in the same pathway to counteract contractions. Accumulation of single-stranded DNA (ssDNA) in the lagging-strand template greatly increases the probability that (GAA)n repeats contract, which in turn promotes repeat instability in rfa1, rad27, and dna2 mutants. Finally, by comparing contraction rates for homopurine-homopyrimidine repeats differing in their mirror symmetry, we found that contractions depend on a repeat’s triplex-forming ability. We propose that accumulation of ssDNA in the lagging-strand template fosters the formation of a triplex between the nascent and fold-back template strands of the repeat. Occasional jumps of DNA polymerase through this triplex hurdle, result in repeat contractions in the nascent lagging strand.
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11
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Kahli M, Osmundson JS, Yeung R, Smith DJ. Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo. Nucleic Acids Res 2019; 47:1814-1822. [PMID: 30541106 PMCID: PMC6393292 DOI: 10.1093/nar/gky1242] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/08/2018] [Accepted: 11/30/2018] [Indexed: 02/07/2023] Open
Abstract
Prior to ligation, each Okazaki fragment synthesized on the lagging strand in eukaryotes must be nucleolytically processed. Nuclease cleavage takes place in the context of 5′ flap structures generated via strand-displacement synthesis by DNA polymerase delta. At least three DNA nucleases: Rad27 (Fen1), Dna2 and Exo1, have been implicated in processing Okazaki fragment flaps. However, neither the contributions of individual nucleases to lagging-strand synthesis nor the structure of the DNA intermediates formed in their absence have been fully defined in vivo. By conditionally depleting lagging-strand nucleases and directly analyzing Okazaki fragments synthesized in vivo in Saccharomyces cerevisiae, we conduct a systematic evaluation of the impact of Rad27, Dna2 and Exo1 on lagging-strand synthesis. We find that Rad27 processes the majority of lagging-strand flaps, with a significant additional contribution from Exo1 but not from Dna2. When nuclease cleavage is impaired, we observe a reduction in strand-displacement synthesis as opposed to the widespread generation of long Okazaki fragment 5′ flaps, as predicted by some models. Further, using cell cycle-restricted constructs, we demonstrate that both the nucleolytic processing and the ligation of Okazaki fragments can be uncoupled from DNA replication and delayed until after synthesis of the majority of the genome is complete.
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Affiliation(s)
- Malik Kahli
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Rani Yeung
- Department of Biology, New York University, New York, NY 10003, USA
| | - Duncan J Smith
- Department of Biology, New York University, New York, NY 10003, USA
- To whom correspondence should be addressed. Tel: +1 212 992 6595;
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Thompson MJ, Gotham VJB, Ciani B, Grasby JA. A conserved loop-wedge motif moderates reaction site search and recognition by FEN1. Nucleic Acids Res 2019; 46:7858-7872. [PMID: 29878258 PMCID: PMC6125683 DOI: 10.1093/nar/gky506] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/23/2018] [Indexed: 12/24/2022] Open
Abstract
DNA replication and repair frequently involve intermediate two-way junction structures with overhangs, or flaps, that must be promptly removed; a task performed by the essential enzyme flap endonuclease 1 (FEN1). We demonstrate a functional relationship between two intrinsically disordered regions of the FEN1 protein, which recognize opposing sides of the junction and order in response to the requisite substrate. Our results inform a model in which short-range translocation of FEN1 on DNA facilitates search for the annealed 3'-terminus of a primer strand, which is recognized by breaking the terminal base pair to generate a substrate with a single nucleotide 3'-flap. This recognition event allosterically signals hydrolytic removal of the 5'-flap through reaction in the opposing junction duplex, by controlling access of the scissile phosphate diester to the active site. The recognition process relies on a highly-conserved 'wedge' residue located on a mobile loop that orders to bind the newly-unpaired base. The unanticipated 'loop-wedge' mechanism exerts control over substrate selection, rate of reaction and reaction site precision, and shares features with other enzymes that recognize irregular DNA structures. These new findings reveal how FEN1 precisely couples 3'-flap verification to function.
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Affiliation(s)
- Mark J Thompson
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
| | - Victoria J B Gotham
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
| | - Barbara Ciani
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
| | - Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
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13
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Tarnauskaitė Ž, Bicknell LS, Marsh JA, Murray JE, Parry DA, Logan CV, Bober MB, de Silva DC, Duker AL, Sillence D, Wise C, Jackson AP, Murina O, Reijns MAM. Biallelic variants in DNA2 cause microcephalic primordial dwarfism. Hum Mutat 2019; 40:1063-1070. [PMID: 31045292 PMCID: PMC6773220 DOI: 10.1002/humu.23776] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/15/2019] [Accepted: 04/28/2019] [Indexed: 11/11/2022]
Abstract
Microcephalic primordial dwarfism (MPD) is a group of rare single-gene disorders characterized by the extreme reduction in brain and body size from early development onwards. Proteins encoded by MPD-associated genes play important roles in fundamental cellular processes, notably genome replication and repair. Here we report the identification of four MPD individuals with biallelic variants in DNA2, which encodes an adenosine triphosphate (ATP)-dependent helicase/nuclease involved in DNA replication and repair. We demonstrate that the two intronic variants (c.1764-38_1764-37ins(53) and c.74+4A>C) found in these individuals substantially impair DNA2 transcript splicing. Additionally, we identify a missense variant (c.1963A>G), affecting a residue of the ATP-dependent helicase domain that is highly conserved between humans and yeast, with the resulting substitution (p.Thr655Ala) predicted to directly impact ATP/ADP (adenosine diphosphate) binding by DNA2. Our findings support the pathogenicity of these variants as biallelic hypomorphic mutations, establishing DNA2 as an MPD disease gene.
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Affiliation(s)
- Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Louise S. Bicknell
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jennie E. Murray
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - David A. Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Clare V. Logan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Michael B. Bober
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - Deepthi C. de Silva
- Department of Physiology, Faculty of MedicineUniversity of KelaniyaColomboSri Lanka
| | - Angela L. Duker
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - David Sillence
- Discipline of Genomic Medicine, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
- Western Sydney Genetics ProgramSydney Children's Hospitals NetworkWestmeadAustralia
| | - Carol Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal ResearchTexas Scottish, Rite Hospital for ChildrenDallasTexas
- McDermott Center for Human Growth and DevelopmentUniversity of Texas, Southwestern Medical CenterDallasTexas
- Department of Orthopaedic SurgeryUniversity of Texas Southwestern Medical CenterDallasTexas
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexas
| | - Andrew P. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Martin A. M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
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14
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Zaher MS, Rashid F, Song B, Joudeh LI, Sobhy MA, Tehseen M, Hingorani MM, Hamdan SM. Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway. Nucleic Acids Res 2019; 46:2956-2974. [PMID: 29420814 PMCID: PMC5888579 DOI: 10.1093/nar/gky082] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/27/2018] [Indexed: 12/11/2022] Open
Abstract
RNA–DNA hybrid primers synthesized by low fidelity DNA polymerase α to initiate eukaryotic lagging strand synthesis must be removed efficiently during Okazaki fragment (OF) maturation to complete DNA replication. In this process, each OF primer is displaced and the resulting 5′-single-stranded flap is cleaved by structure-specific 5′-nucleases, mainly Flap Endonuclease 1 (FEN1), to generate a ligatable nick. At least two models have been proposed to describe primer removal, namely short- and long-flap pathways that involve FEN1 or FEN1 along with Replication Protein A (RPA) and Dna2 helicase/nuclease, respectively. We addressed the question of pathway choice by studying the kinetic mechanism of FEN1 action on short- and long-flap DNA substrates. Using single molecule FRET and rapid quench-flow bulk cleavage assays, we showed that unlike short-flap substrates, which are bound, bent and cleaved within the first encounter between FEN1 and DNA, long-flap substrates can escape cleavage even after DNA binding and bending. Notably, FEN1 can access both substrates in the presence of RPA, but bending and cleavage of long-flap DNA is specifically inhibited. We propose that FEN1 attempts to process both short and long flaps, but occasional missed cleavage of the latter allows RPA binding and triggers the long-flap OF maturation pathway.
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Affiliation(s)
- Manal S Zaher
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Fahad Rashid
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Bo Song
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Luay I Joudeh
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Mohamed A Sobhy
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Muhammad Tehseen
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Samir M Hamdan
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
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15
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Human Exonuclease 1 (EXO1) Regulatory Functions in DNA Replication with Putative Roles in Cancer. Int J Mol Sci 2018; 20:ijms20010074. [PMID: 30585186 PMCID: PMC6337416 DOI: 10.3390/ijms20010074] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/12/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022] Open
Abstract
Human exonuclease 1 (EXO1), a 5'→3' exonuclease, contributes to the regulation of the cell cycle checkpoints, replication fork maintenance, and post replicative DNA repair pathways. These processes are required for the resolution of stalled or blocked DNA replication that can lead to replication stress and potential collapse of the replication fork. Failure to restart the DNA replication process can result in double-strand breaks, cell-cycle arrest, cell death, or cellular transformation. In this review, we summarize the involvement of EXO1 in the replication, DNA repair pathways, cell cycle checkpoints, and the link between EXO1 and cancer.
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16
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Jia PP, Junaid M, Ma YB, Ahmad F, Jia YF, Li WG, Pei DS. Role of human DNA2 (hDNA2) as a potential target for cancer and other diseases: A systematic review. DNA Repair (Amst) 2017; 59:9-19. [PMID: 28903076 DOI: 10.1016/j.dnarep.2017.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/29/2017] [Accepted: 09/01/2017] [Indexed: 11/28/2022]
Abstract
DNA nuclease/helicase 2 (DNA2), a multi-functional protein protecting the high fidelity of genomic transmission, plays critical roles in DNA replication and repair processes. In the maturation of Okazaki fragments, DNA2 acts synergistically with other enzymes to cleave the DNA-RNA primer flaps via different pathways. DNA2 is also involved in the stability of mitochondrial DNA and the maintenance of telomeres. Moreover, DNA2 potentially participates in controlling the cell cycle by repairing the DNA replication faults at main checkpoints. In addition, previous evidences demonstrated that DNA2 also functions in the repair process of DNA damages, such as base excision repair (BER). Currently, large studies revealed the structures and functions of DNA2 in prokaryotes and unicellular eukaryotes, such as bacteria and yeast. However, the studies that highlighted the functions of human DNA2 (hDNA2) and the relationships with other multifunctional proteins are still elusive, and more precise investigations are immensely needed. Therefore, this review mainly encompasses the key functions of DNA2 in human cells with various aspects, especially focusing on the genome integrity, and also generalizes the recent insights to the mechanisms related to the occurrence of cancer and other diseases potentially linked to the mutations in DNA2.
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Affiliation(s)
- Pan-Pan Jia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China; College of Life Science, Henan Normal University, Xinxiang 453007, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhammad Junaid
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Bo Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China
| | - Farooq Ahmad
- Sustainable Development Study Centre, GC University Lahore, Pakistan
| | - Yong-Fang Jia
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Wei-Guo Li
- College of Life Science, Henan Normal University, Xinxiang 453007, China.
| | - De-Sheng Pei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China.
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17
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Bruni F, Lightowlers RN, Chrzanowska-Lightowlers ZM. Human mitochondrial nucleases. FEBS J 2017; 284:1767-1777. [PMID: 27926991 PMCID: PMC5484287 DOI: 10.1111/febs.13981] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/22/2016] [Accepted: 11/30/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria are cytosolic organelles that have many essential roles including ATP production via oxidative phosphorylation, apoptosis, iron‐sulfur cluster biogenesis, heme and steroid synthesis, calcium homeostasis, and regulation of cellular redox state. One of the unique features of these organelles is the presence of an extrachromosomal mitochondrial genome (mtDNA), together with all the machinery required to replicate and transcribe mtDNA. The accurate maintenance of mitochondrial gene expression is essential for correct organellar metabolism, and is in part dependent on the levels of mtDNA and mtRNA, which are regulated by balancing synthesis against degradation. It is clear that although a number of mitochondrial nucleases have been identified, not all those responsible for the degradation of DNA or RNA have been characterized. Recent investigations, however, have revealed the contribution that mutations in the genes coding for these enzymes has made to causing pathogenic mitochondrial diseases.
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Affiliation(s)
- Francesco Bruni
- The Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, UK
| | - Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, UK
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18
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Uhler JP, Thörn C, Nicholls TJ, Matic S, Milenkovic D, Gustafsson CM, Falkenberg M. MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication. Nucleic Acids Res 2016; 44:5861-71. [PMID: 27220468 PMCID: PMC4937333 DOI: 10.1093/nar/gkw468] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 12/17/2022] Open
Abstract
Recently, MGME1 was identified as a mitochondrial DNA nuclease with preference for single-stranded DNA (ssDNA) substrates. Loss-of-function mutations in patients lead to mitochondrial disease with DNA depletion, deletions, duplications and rearrangements. Here, we assess the biochemical role of MGME1 in the processing of flap intermediates during mitochondrial DNA replication using reconstituted systems. We show that MGME1 can cleave flaps to enable efficient ligation of newly replicated DNA strands in combination with POLγ. MGME1 generates a pool of imprecisely cut products (short flaps, nicks and gaps) that are converted to ligatable nicks by POLγ through extension or excision of the 3'-end strand. This is dependent on the 3'-5' exonuclease activity of POLγ which limits strand displacement activity and enables POLγ to back up to the nick by 3'-5' degradation. We also demonstrate that POLγ-driven strand displacement is sufficient to generate DNA- but not RNA-flap substrates suitable for MGME1 cleavage and ligation during replication. Our findings have implications for RNA primer removal models, the 5'-end processing of nascent DNA at OriH, and DNA repair.
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Affiliation(s)
- Jay P Uhler
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Christian Thörn
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Thomas J Nicholls
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Stanka Matic
- Max Planck Institute for Biology of Ageing, 50391 Cologne, Germany
| | | | - Claes M Gustafsson
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Maria Falkenberg
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
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19
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A euryarchaeal histone modulates strand displacement synthesis by replicative DNA polymerases. SCIENCE CHINA-LIFE SCIENCES 2016; 59:709-16. [DOI: 10.1007/s11427-016-5076-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/29/2016] [Indexed: 10/21/2022]
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20
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Zhou C, Pourmal S, Pavletich NP. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa. eLife 2015; 4. [PMID: 26491943 PMCID: PMC4716839 DOI: 10.7554/elife.09832] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/20/2015] [Indexed: 12/04/2022] Open
Abstract
The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5’ end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5’ but not 3’ end, explaining how Rpa regulates cleavage polarity. DOI:http://dx.doi.org/10.7554/eLife.09832.001 DNA carries the genetic information that is essential for organisms to survive and reproduce. It is made of two strands that twist together to form a double helix. However, these strands can be damaged when the DNA is copied before a cell divides, or by exposure to radiation or hazardous chemicals. To prevent this damage from causing serious harm to an organism, cells activate processes that rapidly repair the damaged DNA. “Homologous recombination” is one way in which cells can repair damage that has caused both strands of the DNA to break in a particular place. In the first step, several enzymes trim one of the two DNA strands at each broken end to leave single stranded “tails”. Dna2 is one enzyme that is involved in making these tails, but it can only bind to single-stranded DNA so it only acts after another enzyme has made some initial cuts. The exposed single stranded DNA then searches for an intact copy of itself elsewhere in the genome, which promotes its repair. It is important that only one of the two DNA strands is trimmed at each end otherwise the repair will fail. A protein called Rpa is bound to the DNA and is required for Dna2 to correctly trim the DNA. However, it is not clear exactly how Rpa2 regulates Dna2. Zhou et al. used a technique called X-ray crystallography to analyze the three-dimensional structures of Dna2 when it is bound to single stranded DNA and when it is bound to Rpa. The experiments show that Dna2 adopts a cylindrical shape with a tunnel through which the single-stranded DNA passes through. The region of Dna2 that is capable of trimming DNA – which is called the nuclease domain – is embedded within the tunnel. The entrance to the tunnel is too narrow to allow double-stranded DNA to enter, so this explains why Dna2 can only act on double-stranded DNA that already has a small single-stranded section at the end. Inside the tunnel, Dna2 displaces Rpa from one of the strands, which allows Dna2 to trim the DNA. However, other molecules of Rpa remain firmly bound to the other strand to protect it from Dna2. These enzymes also act in a similar way to trim DNA before it is copied in preparation for cell division. Zhou et al.’s findings provide an explanation for how Rpa determines which strand of DNA is trimmed by Dna2. Further work is needed to understand how Dna2 and Rpa work with other enzymes to trim DNA. DOI:http://dx.doi.org/10.7554/eLife.09832.002
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Affiliation(s)
- Chun Zhou
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sergei Pourmal
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Nikola P Pavletich
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, United States
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21
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Chamieh H, Ibrahim H, Kozah J. Genome-wide identification of SF1 and SF2 helicases from archaea. Gene 2015; 576:214-28. [PMID: 26456193 DOI: 10.1016/j.gene.2015.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 08/13/2015] [Accepted: 10/04/2015] [Indexed: 11/26/2022]
Abstract
Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E. coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaeota and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions.
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Affiliation(s)
- Hala Chamieh
- Faculty of Science, Department of Biology, Lebanese University, Tripoli, Lebanon; Centre AZM pour la Recherche en Biotechnologie et ses Applications, Laboratoire de Biotechnologie Appliquée, Ecole Doctorale Sciences et Technologies, Mitein Street, Tripoli, Lebanon.
| | - Hiba Ibrahim
- Faculty of Science, Department of Environmental and Biological Science, Beirut Arab University, Tripoli, Lebanon
| | - Juliana Kozah
- Faculty of Science, Université Saint Esprit de Kaslik, Jounieh, Lebanon
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22
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Primer removal during mammalian mitochondrial DNA replication. DNA Repair (Amst) 2015; 34:28-38. [PMID: 26303841 DOI: 10.1016/j.dnarep.2015.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/17/2022]
Abstract
The small circular mitochondrial genome in mammalian cells is replicated by a dedicated replisome, defects in which can cause mitochondrial disease in humans. A fundamental step in mitochondrial DNA (mtDNA) replication and maintenance is the removal of the RNA primers needed for replication initiation. The nucleases RNase H1, FEN1, DNA2, and MGME1 have been implicated in this process. Here we review the role of these nucleases in the light of primer removal pathways in mitochondria, highlight associations with disease, as well as consider the implications for mtDNA replication initiation.
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23
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Ahmed N, Ronchi D, Comi GP. Genes and Pathways Involved in Adult Onset Disorders Featuring Muscle Mitochondrial DNA Instability. Int J Mol Sci 2015; 16:18054-76. [PMID: 26251896 PMCID: PMC4581235 DOI: 10.3390/ijms160818054] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 12/31/2022] Open
Abstract
Replication and maintenance of mtDNA entirely relies on a set of proteins encoded by the nuclear genome, which include members of the core replicative machinery, proteins involved in the homeostasis of mitochondrial dNTPs pools or deputed to the control of mitochondrial dynamics and morphology. Mutations in their coding genes have been observed in familial and sporadic forms of pediatric and adult-onset clinical phenotypes featuring mtDNA instability. The list of defects involved in these disorders has recently expanded, including mutations in the exo-/endo-nuclease flap-processing proteins MGME1 and DNA2, supporting the notion that an enzymatic DNA repair system actively takes place in mitochondria. The results obtained in the last few years acknowledge the contribution of next-generation sequencing methods in the identification of new disease loci in small groups of patients and even single probands. Although heterogeneous, these genes can be conveniently classified according to the pathway to which they belong. The definition of the molecular and biochemical features of these pathways might be helpful for fundamental knowledge of these disorders, to accelerate genetic diagnosis of patients and the development of rational therapies. In this review, we discuss the molecular findings disclosed in adult patients with muscle pathology hallmarked by mtDNA instability.
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Affiliation(s)
- Naghia Ahmed
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Centre, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, via Francesco Sforza 35, Milan 20122, Italy.
| | - Dario Ronchi
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Centre, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, via Francesco Sforza 35, Milan 20122, Italy.
| | - Giacomo Pietro Comi
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Centre, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, via Francesco Sforza 35, Milan 20122, Italy.
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24
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Human exonuclease 1 (EXO1) activity characterization and its function on flap structures. Biosci Rep 2015; 35:BSR20150058. [PMID: 26182368 PMCID: PMC4613700 DOI: 10.1042/bsr20150058] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/24/2015] [Indexed: 11/26/2022] Open
Abstract
We report biochemical characterization of human full-length EXO1 including thermodynamic stability and flap activity on DNA flap structures. Our results reveal novel mechanistic insights into the processing of flap structures and a possible role of EXO1 in strand displacement. Human exonuclease 1 (EXO1) is involved in multiple DNA metabolism processes, including DNA repair and replication. Most of the fundamental roles of EXO1 have been described in yeast. Here, we report a biochemical characterization of human full-length EXO1. Prior to assay EXO1 on different DNA flap structures, we determined factors essential for the thermodynamic stability of EXO1. We show that enzymatic activity and stability of EXO1 on DNA is modulated by temperature. By characterization of EXO1 flap activity using various DNA flap substrates, we show that EXO1 has a strong capacity for degrading double stranded DNA and has a modest endonuclease or 5′ flap activity. Furthermore, we report novel mechanistic insights into the processing of flap structures, showing that EXO1 preferentially cleaves one nucleotide inwards in a double stranded region of a forked and nicked DNA flap substrates, suggesting a possible role of EXO1 in strand displacement.
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25
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Ngo GHP, Balakrishnan L, Dubarry M, Campbell JL, Lydall D. The 9-1-1 checkpoint clamp stimulates DNA resection by Dna2-Sgs1 and Exo1. Nucleic Acids Res 2014; 42:10516-28. [PMID: 25122752 PMCID: PMC4176354 DOI: 10.1093/nar/gku746] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) at DNA ends is an important regulator of the DNA damage response. Resection, the generation of ssDNA, affects DNA damage checkpoint activation, DNA repair pathway choice, ssDNA-associated mutation and replication fork stability. In eukaryotes, extensive DNA resection requires the nuclease Exo1 and nuclease/helicase pair: Dna2 and Sgs1BLM. How Exo1 and Dna2-Sgs1BLM coordinate during resection remains poorly understood. The DNA damage checkpoint clamp (the 9-1-1 complex) has been reported to play an important role in stimulating resection but the exact mechanism remains unclear. Here we show that the human 9-1-1 complex enhances the cleavage of DNA by both DNA2 and EXO1 in vitro, showing that the resection-stimulatory role of the 9-1-1 complex is direct. We also show that in Saccharomyces cerevisiae, the 9-1-1 complex promotes both Dna2-Sgs1 and Exo1-dependent resection in response to uncapped telomeres. Our results suggest that the 9-1-1 complex facilitates resection by recruiting both Dna2-Sgs1 and Exo1 to sites of resection. This activity of the 9-1-1 complex in supporting resection is strongly inhibited by the checkpoint adaptor Rad953BP1. Our results provide important mechanistic insights into how DNA resection is regulated by checkpoint proteins and have implications for genome stability in eukaryotes.
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Affiliation(s)
- Greg H P Ngo
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Marion Dubarry
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Judith L Campbell
- Divisions of Biology and Chemistry, Caltech, Braun Laboratories, Pasadena, CA 91125, USA
| | - David Lydall
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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Sun F, Huang L. Sulfolobus chromatin proteins modulate strand displacement by DNA polymerase B1. Nucleic Acids Res 2013; 41:8182-95. [PMID: 23821667 PMCID: PMC3783171 DOI: 10.1093/nar/gkt588] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Strand displacement by a DNA polymerase serves a key role in Okazaki fragment maturation, which involves displacement of the RNA primer of the preexisting Okazaki fragment into a flap structure, and subsequent flap removal and fragment ligation. We investigated the role of Sulfolobus chromatin proteins Sso7d and Cren7 in strand displacement by DNA polymerase B1 (PolB1) from the hyperthermophilic archaeon Sulfolobus solfataricus. PolB1 showed a robust strand displacement activity and was capable of synthesizing thousands of nucleotides on a DNA-primed 72-nt single-stranded circular DNA template. This activity was inhibited by both Sso7d and Cren7, which limited the flap length to 3–4 nt at saturating concentrations. However, neither protein inhibited RNA displacement on an RNA-primed single-stranded DNA minicircle by PolB1. Strand displacement remained sensitive to modulation by the chromatin proteins when PolB1 was in association with proliferating cell nuclear antigen. Inhibition of DNA instead of RNA strand displacement by the chromatin proteins is consistent with the finding that double-stranded DNA was more efficiently bound and stabilized than an RNA:DNA duplex by these proteins. Our results suggest that Sulfolobus chromatin proteins modulate strand displacement by PolB1, permitting efficient removal of the RNA primer while inhibiting excessive displacement of the newly synthesized DNA strand during Okazaki fragment maturation.
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Affiliation(s)
- Fei Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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27
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Szczesny RJ, Hejnowicz MS, Steczkiewicz K, Muszewska A, Borowski LS, Ginalski K, Dziembowski A. Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels. Nucleic Acids Res 2013; 41:3144-61. [PMID: 23358826 PMCID: PMC3597694 DOI: 10.1093/nar/gkt029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the human mitochondrial genome has been investigated for several decades, the proteins responsible for its replication and expression, especially nucleolytic enzymes, are poorly described. Here, we characterized a novel putative PD-(D/E)XK nuclease encoded by the human C20orf72 gene named Ddk1 for its predicted catalytic residues. We show that Ddk1 is a mitochondrially localized metal-dependent DNase lacking detectable ribonuclease activity. Ddk1 degrades DNA mainly in a 3'-5' direction with a strong preference for single-stranded DNA. Interestingly, Ddk1 requires free ends for its activity and does not degrade circular substrates. In addition, when a chimeric RNA-DNA substrate is provided, Ddk1 can slide over the RNA fragment and digest DNA endonucleolytically. Although the levels of the mitochondrial DNA are unchanged on RNAi-mediated depletion of Ddk1, the mitochondrial single-stranded DNA molecule (7S DNA) accumulates. On the other hand, overexperssion of Ddk1 decreases the levels of 7S DNA, suggesting an important role of the protein in 7S DNA regulation. We propose a structural model of Ddk1 and discuss its similarity to other PD-(D/E)XK superfamily members.
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Affiliation(s)
- Roman J Szczesny
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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28
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Waisertreiger ISR, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:699-724. [PMID: 23055184 PMCID: PMC3893020 DOI: 10.1002/em.21735] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 06/01/2023]
Abstract
The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ϵ, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.
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Affiliation(s)
- Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Victoria G. Liston
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Miriam R. Menezes
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Igor B. Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Youri. I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
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29
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Pokharel S, Campbell JL. Cross talk between the nuclease and helicase activities of Dna2: role of an essential iron-sulfur cluster domain. Nucleic Acids Res 2012; 40:7821-30. [PMID: 22684504 PMCID: PMC3439918 DOI: 10.1093/nar/gks534] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dna2 nuclease/helicase is a multitasking protein involved in DNA replication and recombinational repair, and it is important for preservation of genomic stability. Yeast Dna2 protein contains a conserved putative Fe-S (iron-sulfur) cluster signature motif spanning the nuclease active site. We show that this motif is indeed an Fe-S cluster domain. Mutation of cysteines involved in metal coordination greatly reduces not just the nuclease activity but also the ATPase activity of Dna2, suggesting that the nuclease and helicase activities are coupled. The affinity for DNA is not significantly reduced, but binding mode in the C to A mutants is altered. Remarkably, a point mutation (P504S), proximal to the Fe-S cluster domain, which renders cells temperature sensitive, closely mimics the global defects of the Fe-S cluster mutation itself. This points to an important role of this conserved proline residue in stabilizing the Fe-S cluster. The C to A mutants are deficient in DNA replication and repair in vivo, and, strikingly, the degree to which they are defective correlates directly with degree of loss of enzymatic activity. Taken together with previous results showing that mutations in the ATP domain affect nuclease function, our results provide a new mechanistic paradigm for coupling between nuclease and helicase modules fused in the same polypeptide.
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Affiliation(s)
- Subhash Pokharel
- Braun Laboratories, 147-75, California Institute of Technology, Pasadena, CA 91125, USA
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