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Weiss T, Kumar J, Chen C, Guo S, Schlegel O, Lutterman J, Ling K, Zhang F. Dual activities of an X-family DNA polymerase regulate CRISPR-induced insertional mutagenesis across species. Nat Commun 2024; 15:6293. [PMID: 39060288 PMCID: PMC11282277 DOI: 10.1038/s41467-024-50676-4] [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: 01/10/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The canonical non-homologous end joining (c-NHEJ) repair pathway, generally viewed as stochastic, has recently been shown to produce predictable outcomes in CRISPR-Cas9 mutagenesis. This predictability, mainly in 1-bp insertions and small deletions, has led to the development of in-silico prediction programs for various animal species. However, the predictability of CRISPR-induced mutation profiles across species remained elusive. Comparing CRISPR-Cas9 repair outcomes between human and plant species reveals significant differences in 1-bp insertion profiles. The high predictability observed in human cells links to the template-dependent activity of human Polλ. Yet plant Polλ exhibits dual activities, generating 1-bp insertions through both templated and non-templated manners. Polλ knockout in plants leads to deletion-only mutations, while its overexpression enhances 1-bp insertion rates. Two conserved motifs are identified to modulate plant Polλ's dual activities. These findings unveil the mechanism behind species-specific CRISPR-Cas9-induced insertion profiles and offer strategies for predictable, precise genome editing through c-NHEJ.
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Affiliation(s)
- Trevor Weiss
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shengsong Guo
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Oliver Schlegel
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Lutterman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA.
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA.
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2
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Mentegari E, Bertoletti F, Kissova M, Zucca E, Galli S, Tagliavini G, Garbelli A, Maffia A, Bione S, Ferrari E, d’Adda di Fagagna F, Francia S, Sabbioneda S, Chen LY, Lingner J, Bergoglio V, Hoffmann JS, Hübscher U, Crespan E, Maga G. A Role for Human DNA Polymerase λ in Alternative Lengthening of Telomeres. Int J Mol Sci 2021; 22:ijms22052365. [PMID: 33673424 PMCID: PMC7956399 DOI: 10.3390/ijms22052365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Telomerase negative cancer cell types use the Alternative Lengthening of Telomeres (ALT) pathway to elongate telomeres ends. Here, we show that silencing human DNA polymerase (Pol λ) in ALT cells represses ALT activity and induces telomeric stress. In addition, replication stress in the absence of Pol λ, strongly affects the survival of ALT cells. In vitro, Pol λ can promote annealing of even a single G-rich telomeric repeat to its complementary strand and use it to prime DNA synthesis. The noncoding telomeric repeat containing RNA TERRA and replication protein A negatively regulate this activity, while the Protection of Telomeres protein 1 (POT1)/TPP1 heterodimer stimulates Pol λ. Pol λ associates with telomeres and colocalizes with TPP1 in cells. In summary, our data suggest a role of Pol λ in the maintenance of telomeres by the ALT mechanism.
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Affiliation(s)
- Elisa Mentegari
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Federica Bertoletti
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Miroslava Kissova
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elisa Zucca
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Galli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Giulia Tagliavini
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Antonio Maffia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Bione
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Fabrizio d’Adda di Fagagna
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- IFOM-The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Sofia Francia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Liuh-Yow Chen
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Valerie Bergoglio
- UMR1037 INSERM, Cancer Research Center of Toulouse, 2 Avenue Curien, 31037 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Ulrich Hübscher
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
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3
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Trimidal SG, Benjamin R, Bae JE, Han MV, Kong E, Singer A, Williams TS, Yang B, Schiller MR. Can Designer Indels Be Tailored by Gene Editing?: Can Indels Be Customized? Bioessays 2019; 41:e1900126. [PMID: 31693213 PMCID: PMC7202862 DOI: 10.1002/bies.201900126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/01/2019] [Indexed: 12/23/2022]
Abstract
Genome editing with engineered nucleases (GEENs) introduce site-specific DNA double-strand breaks (DSBs) and repairs DSBs via nonhomologous end-joining (NHEJ) pathways that eventually create indels (insertions/deletions) in a genome. Whether the features of indels resulting from gene editing could be customized is asked. A review of the literature reveals how gene editing technologies via NHEJ pathways impact gene editing. The survey consolidates a body of literature that suggests that the type (insertion, deletion, and complex) and the approximate length of indel edits can be somewhat customized with different GEENs and by manipulating the expression of key NHEJ genes. Structural data suggest that binding of GEENs to DNA may interfere with binding of key components of DNA repair complexes, favoring either classical- or alternative-NHEJ. The hypotheses have some limitations, but if validated, will enable scientists to better control indel makeup, holding promise for basic science and clinical applications of gene editing. Also see the video abstract here https://youtu.be/vTkJtUsLi3w.
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Affiliation(s)
- Sara G Trimidal
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Ronald Benjamin
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Ji Eun Bae
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Mira V Han
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Elizabeth Kong
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Aaron Singer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Tyler S Williams
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Bing Yang
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Martin R Schiller
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
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4
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Thomas C, Rusanov T, Hoang T, Augustin T, Kent T, Gaspar I, Pomerantz RT. One-step enzymatic modification of RNA 3' termini using polymerase θ. Nucleic Acids Res 2019; 47:3272-3283. [PMID: 30818397 PMCID: PMC6468238 DOI: 10.1093/nar/gkz029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 01/13/2019] [Accepted: 02/13/2019] [Indexed: 11/27/2022] Open
Abstract
Site-specific modification of synthetic and cellular RNA such as with specific nucleobases, fluorophores and attachment chemistries is important for a variety of basic and applied research applications. However, simple and efficient methods to modify RNA such as at the 3' terminus with specific nucleobases or nucleotide analogs conjugated to various chemical moieties are lacking. Here, we develop and characterize a one-step enzymatic method to modify RNA 3' termini using recombinant human polymerase theta (Polθ). We demonstrate that Polθ efficiently adds 30-50 2'-deoxyribonucleotides to the 3' terminus of RNA molecules of various lengths and sequences, and extends RNA 3' termini with an assortment of 2'-deoxy and 2',3'-dideoxy ribonucleotide analogs containing functional chemistries, such as high affinity attachment moieties and fluorophores. In contrast to Polθ, terminal deoxynucleotidyl transferase (TdT) is unable to use RNA as a substrate altogether. Overall, Polθ shows a strong preference for adding deoxyribonucleotides to RNA, but can also add ribonucleotides with relatively high efficiency in particular sequence contexts. We anticipate that this unique activity of Polθ will become invaluable for applications requiring 3' terminal modification of RNA and potentially enzymatic synthesis of RNA.
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Affiliation(s)
- Crystal Thomas
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Timur Rusanov
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Trung Hoang
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Taurai Augustin
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Tatiana Kent
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Imre Gaspar
- European Molecular Biology Laboratory, Heidelberg, Meyerhofstrasse 1, 69117, Germany
| | - Richard T Pomerantz
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
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5
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A versatile method for the UVA-induced cross-linking of acetophenone- or benzophenone-functionalized DNA. Sci Rep 2018; 8:16484. [PMID: 30405165 PMCID: PMC6220319 DOI: 10.1038/s41598-018-34892-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/25/2018] [Indexed: 11/08/2022] Open
Abstract
Bioconjugation, biosensing, bioimaging, bionanomaterials, etc., are only a few examples of application of functionalized DNA. Since base-modified nucleic acids contribute not only to a broad range of biotechnological fields but also to the understanding of various cellular processes, it is crucial to design novel modifications with unique properties. Here, we demonstrate the utilization of N4-cytidine modified oligonucleotides, which contain reactive acetophenone (AP) or benzophenone (BP) groups, for the UV-induced cross-linking. We find that terminal deoxynucleotidyl transferase-mediated 3'-tailing using AP/BP-containing modified nucleotides generates photoactive DNA, suitable for a straightforward covalent cross-linking with both interacting proteins and a variety of well-known solid polymeric supports. Moreover, we show that AP/BP-functionalization of nucleic acid molecules induces an efficient cross-linking upon exposure to UVA light. Our findings reveal that 3'-tailed single-stranded DNA bearing AP/BP-moieties is easily photoimmobilized onto untreated polystyrene, polypropylene, polylactate, polydimethylsiloxane, sol-gel and borosilicate glass substrates. Furthermore, we demonstrate that such immobilized DNA probes can be further used for successful hybridization of complementary DNA targets. Our results establish novel N4-cytosine nucleobase modifications as photoreactive labels and suggest an effortless approach for photoimmobilization of nucleic acids.
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6
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Randrianjatovo-Gbalou I, Rosario S, Sismeiro O, Varet H, Legendre R, Coppée JY, Huteau V, Pochet S, Delarue M. Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries. Nucleic Acids Res 2018; 46:6271-6284. [PMID: 29788485 PMCID: PMC6158600 DOI: 10.1093/nar/gky413] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/12/2018] [Accepted: 05/04/2018] [Indexed: 12/17/2022] Open
Abstract
Nucleic acid aptamers, especially RNA, exhibit valuable advantages compared to protein therapeutics in terms of size, affinity and specificity. However, the synthesis of libraries of large random RNAs is still difficult and expensive. The engineering of polymerases able to directly generate these libraries has the potential to replace the chemical synthesis approach. Here, we start with a DNA polymerase that already displays a significant template-free nucleotidyltransferase activity, human DNA polymerase theta, and we mutate it based on the knowledge of its three-dimensional structure as well as previous mutational studies on members of the same polA family. One mutant exhibited a high tolerance towards ribonucleotides (NTPs) and displayed an efficient ribonucleotidyltransferase activity that resulted in the assembly of long RNA polymers. HPLC analysis and RNA sequencing of the products were used to quantify the incorporation of the four NTPs as a function of initial NTP concentrations and established the randomness of each generated nucleic acid sequence. The same mutant revealed a propensity to accept other modified nucleotides and to extend them in long fragments. Hence, this mutant can deliver random natural and modified RNA polymers libraries ready to use for SELEX, with custom lengths and balanced or unbalanced ratios.
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Affiliation(s)
- Irina Randrianjatovo-Gbalou
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sandrine Rosario
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Hugo Varet
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rachel Legendre
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Jean-Yves Coppée
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Huteau
- Unité de Chimie et Biocatalyse, CNRS UMR 3523, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, CNRS UMR 3523, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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Vaisman A, Woodgate R. Ribonucleotide discrimination by translesion synthesis DNA polymerases. Crit Rev Biochem Mol Biol 2018; 53:382-402. [PMID: 29972306 DOI: 10.1080/10409238.2018.1483889] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The well-being of all living organisms relies on the accurate duplication of their genomes. This is usually achieved by highly elaborate replicase complexes which ensure that this task is accomplished timely and efficiently. However, cells often must resort to the help of various additional "specialized" DNA polymerases that gain access to genomic DNA when replication fork progression is hindered. One such specialized polymerase family consists of the so-called "translesion synthesis" (TLS) polymerases; enzymes that have evolved to replicate damaged DNA. To fulfill their main cellular mission, TLS polymerases often must sacrifice precision when selecting nucleotide substrates. Low base-substitution fidelity is a well-documented inherent property of these enzymes. However, incorrect nucleotide substrates are not only those which do not comply with Watson-Crick base complementarity, but also those whose sugar moiety is incorrect. Does relaxed base-selectivity automatically mean that the TLS polymerases are unable to efficiently discriminate between ribonucleoside triphosphates and deoxyribonucleoside triphosphates that differ by only a single atom? Which strategies do TLS polymerases employ to select suitable nucleotide substrates? In this review, we will collate and summarize data accumulated over the past decade from biochemical and structural studies, which aim to answer these questions.
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Affiliation(s)
- Alexandra Vaisman
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Roger Woodgate
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
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8
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Shapla UM, Solayman M, Alam N, Khalil MI, Gan SH. 5-Hydroxymethylfurfural (HMF) levels in honey and other food products: effects on bees and human health. Chem Cent J 2018; 12:35. [PMID: 29619623 PMCID: PMC5884753 DOI: 10.1186/s13065-018-0408-3] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/27/2018] [Indexed: 02/07/2023] Open
Abstract
An organic compound known as 5-hydroxymethylfurfural (HMF) is formed from reducing sugars in honey and various processed foods in acidic environments when they are heated through the Maillard reaction. In addition to processing, storage conditions affect the formation HMF, and HMF has become a suitable indicator of honey quality. HMF is easily absorbed from food through the gastrointestinal tract and, upon being metabolized into different derivatives, is excreted via urine. In addition to exerting detrimental effects (mutagenic, genotoxic, organotoxic and enzyme inhibitory), HMF, which is converted to a non-excretable, genotoxic compound called 5-sulfoxymethylfurfural, is beneficial to human health by providing antioxidative, anti-allergic, anti-inflammatory, anti-hypoxic, anti-sickling, and anti-hyperuricemic effects. Therefore, HMF is a neo-forming contaminant that draws great attention from scientists. This review compiles updated information regarding HMF formation, detection procedures, mitigation strategies and effects of HMF on honey bees and human health.
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Affiliation(s)
- Ummay Mahfuza Shapla
- Laboratory of Preventive and Integrative Bio-medicine, Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Solayman
- Laboratory of Preventive and Integrative Bio-medicine, Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh. .,Department of Biochemistry, Primeasia University, Banani, 1213, Bangladesh.
| | - Nadia Alam
- School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Md Ibrahim Khalil
- Laboratory of Preventive and Integrative Bio-medicine, Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh.,School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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9
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DNA polymerases β and λ and their roles in cell. DNA Repair (Amst) 2015; 29:112-26. [DOI: 10.1016/j.dnarep.2015.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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10
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Strittmatter T, Brockmann A, Pott M, Hantusch A, Brunner T, Marx A. Expanding the scope of human DNA polymerase λ and β inhibitors. ACS Chem Biol 2014; 9:282-90. [PMID: 24171552 DOI: 10.1021/cb4007562] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The exact biological functions of individual DNA polymerases still await clarification, and therefore appropriate reagents to probe their respective functions are required. In the present study, we report the development of a highly potent series of human DNA polymerase λ and β (pol λ and β) inhibitors based on the rhodanine scaffold. Both enzymes are involved in DNA repair and are thus considered as future drug targets. We expanded the chemical diversity of the small-molecule inhibitors arising from a high content screening and designed and synthesized 30 novel analogues. By biochemical evaluation, we discovered 23 highly active compounds against pol λ. Importantly, 10 of these small-molecules selectively inhibited pol λ and not the homologous pol β. We discovered 14 small-molecules that target pol β and found out that they are more potent than known inhibitors. We also investigated whether the discovered compounds sensitize cancer cells toward DNA-damaging reagents. Thus, we cotreated human colorectal cancer cells (Caco-2) with the small-molecule inhibitors and hydrogen peroxide or the approved drug temozolomide. Interestingly, the tested compounds sensitized Caco-2 cells to both genotoxic agents in a DNA repair pathway-dependent manner.
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Affiliation(s)
- Tobias Strittmatter
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Anette Brockmann
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Moritz Pott
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Annika Hantusch
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Thomas Brunner
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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11
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Kanagaraj R, Parasuraman P, Mihaljevic B, van Loon B, Burdova K, König C, Furrer A, Bohr VA, Hübscher U, Janscak P. Involvement of Werner syndrome protein in MUTYH-mediated repair of oxidative DNA damage. Nucleic Acids Res 2012; 40:8449-59. [PMID: 22753033 PMCID: PMC3458577 DOI: 10.1093/nar/gks648] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reactive oxygen species constantly generated as by-products of cellular metabolism readily attack genomic DNA creating mutagenic lesions such as 7,8-dihydro-8-oxo-guanine (8-oxo-G) that promote aging. 8-oxo-G:A mispairs arising during DNA replication are eliminated by base excision repair initiated by the MutY DNA glycosylase homologue (MUTYH). Here, by using formaldehyde crosslinking in mammalian cell extracts, we demonstrate that the WRN helicase/exonuclease defective in the premature aging disorder Werner syndrome (WS) is recruited to DNA duplex containing an 8-oxo-G:A mispair in a manner dependent on DNA polymerase λ (Polλ) that catalyzes accurate DNA synthesis over 8-oxo-G. Similarly, by immunofluorescence, we show that Polλ is required for accumulation of WRN at sites of 8-oxo-G lesions in human cells. Moreover, we show that nuclear focus formation of WRN and Polλ induced by oxidative stress is dependent on ongoing DNA replication and on the presence of MUTYH. Cell viability assays reveal that depletion of MUTYH suppresses the hypersensitivity of cells lacking WRN and/or Polλ to oxidative stress. Biochemical studies demonstrate that WRN binds to the catalytic domain of Polλ and specifically stimulates DNA gap filling by Polλ over 8-oxo-G followed by strand displacement synthesis. Our results suggest that WRN promotes long-patch DNA repair synthesis by Polλ during MUTYH-initiated repair of 8-oxo-G:A mispairs.
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Affiliation(s)
- Radhakrishnan Kanagaraj
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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12
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Skosareva LV, Lebedeva NA, Rechkunova NI, Kolbanovskiy A, Geacintov NE, Lavrik OI. Human DNA polymerase λ catalyzes lesion bypass across benzo[a]pyrene-derived DNA adduct during base excision repair. DNA Repair (Amst) 2012; 11:367-73. [PMID: 22317757 DOI: 10.1016/j.dnarep.2012.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/15/2011] [Accepted: 01/03/2012] [Indexed: 11/17/2022]
Abstract
The combined action of oxidative stress and genotoxic polycyclic aromatic hydrocarbons derivatives can lead to cluster-type DNA damage that includes both a modified nucleotide and a bulky lesion. As an example, we investigated the possibility of repair of an AP site located opposite a minor groove-positioned (+)-trans-BPDE-dG or a base-displaced intercalated (+)-cis-BPDE-dG adduct (BP lesion) by a BER system. Oligonucleotides with single uracil residues in certain positions were annealed with complementary oligonucleotides bearing either a cis- or trans-BP adduct. The resulting DNA duplexes contained dU either directly opposite the modified dG or shifted to adjacent 5' (-1) or 3' (+1) positions. Digestion with uracil DNA glycosylase was utilized to generate AP sites which were then hydrolyzed by APE1, and the resulting gaps were processed by DNA polymerase β (Polβ) or λ (Polλ). The AP sites in position -1 can be repaired effectively using APE1 and Polβ or Polλ. The AP sites opposite the BP lesions can be repaired using Polλ in the case of cis- but not the trans-isomeric adduct. The AP sites in position +1 are the most difficult to repair. In the case of the AP site located in position +1, the activity of Polλ does not depend on the stereoisomeric properties of the BP lesions and dCTP is the preferred inserted substrate in both cases. The capability of Polλ to introduce the correct dNTP opposite the cis-BP-dG adduct in gap filling reactions suggests that this polymerase may play a specialized role in the process of repair of these kinds of lesions.
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Affiliation(s)
- Lidia V Skosareva
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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13
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Knobel PA, Marti TM. Translesion DNA synthesis in the context of cancer research. Cancer Cell Int 2011; 11:39. [PMID: 22047021 PMCID: PMC3224763 DOI: 10.1186/1475-2867-11-39] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 11/02/2011] [Indexed: 11/17/2022] Open
Abstract
During cell division, replication of the genomic DNA is performed by high-fidelity DNA polymerases but these error-free enzymes can not synthesize across damaged DNA. Specialized DNA polymerases, so called DNA translesion synthesis polymerases (TLS polymerases), can replicate damaged DNA thereby avoiding replication fork breakdown and subsequent chromosomal instability. We focus on the involvement of mammalian TLS polymerases in DNA damage tolerance mechanisms. In detail, we review the discovery of TLS polymerases and describe the molecular features of all the mammalian TLS polymerases identified so far. We give a short overview of the mechanisms that regulate the selectivity and activity of TLS polymerases. In addition, we summarize the current knowledge how different types of DNA damage, relevant either for the induction or treatment of cancer, are bypassed by TLS polymerases. Finally, we elucidate the relevance of TLS polymerases in the context of cancer therapy.
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Affiliation(s)
- Philip A Knobel
- Laboratory of Molecular Oncology, Clinic and Polyclinic of Oncology, University Hospital Zürich, Häldeliweg 4, CH-8044 Zürich, Switzerland.
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14
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Crespan E, Garbelli A, Amoroso A, Maga G. Exploiting the nucleotide substrate specificity of repair DNA polymerases to develop novel anticancer agents. Molecules 2011; 16:7994-8019. [PMID: 21926946 PMCID: PMC6264456 DOI: 10.3390/molecules16097994] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/26/2011] [Accepted: 09/13/2011] [Indexed: 11/16/2022] Open
Abstract
The genome is constantly exposed to mutations that can originate during replication or as a result of the action of both endogenous and/or exogenous damaging agents [such as reactive oxygen species (ROS), UV light, genotoxic environmental compounds, etc.]. Cells have developed a set of specialized mechanisms to counteract this mutational burden. Many cancer cells have defects in one or more DNA repair pathways, hence they rely on a narrower set of specialized DNA repair mechanisms than normal cells. Inhibiting one of these pathways in the context of an already DNA repair-deficient genetic background, will be more toxic to cancer cells than to normal cells, a concept recently exploited in cancer chemotherapy by the synthetic lethality approach. Essential to all DNA repair pathways are the DNA pols. Thus, these enzymes are being regarded as attractive targets for the development of specific inhibitors of DNA repair in cancer cells. In this review we examine the current state-of-the-art in the development of nucleotide analogs as inhibitors of repair DNA polymerases.
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Affiliation(s)
- Emmanuele Crespan
- DNA Enzymology & Molecular Virology, Insititute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy.
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15
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Strittmatter T, Bareth B, Immel TA, Huhn T, Mayer TU, Marx A. Small Molecule Inhibitors of Human DNA Polymerase λ. ACS Chem Biol 2011; 6:314-9. [PMID: 21194240 DOI: 10.1021/cb100382m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To discover chemical probes to further under-stand the function of individual DNA polymerases, we established a generally applicable high-throughput screening. By applying this technique we discovered three novel inhibitor classes of human DNA polymerase λ (DNA Pol λ), a key enzyme to maintain the genetic integrity of the genome. The rhodanines, classified as an excellent drug scaffold, were found to be the most potent inhibitors for DNA Pol λ. Importantly, they are up to 10 times less active against the highly similar DNA polymerase β. We investigated basic structure activity relationships. Furthermore, the rhodanines showed pharmacological activity in two human cancer cell lines. So the here reported small molecules could serve as useful DNA Pol λ probes and might serve as starting point to develop novel therapeutic agents.
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Affiliation(s)
- Tobias Strittmatter
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Bettina Bareth
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Timo A. Immel
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Thomas Huhn
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Thomas U. Mayer
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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16
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Markkanen E, van Loon B, Ferrari E, Hübscher U. Ubiquitylation of DNA polymerase λ. FEBS Lett 2011; 585:2826-30. [PMID: 21486570 DOI: 10.1016/j.febslet.2011.03.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 12/26/2022]
Abstract
DNA polymerase (pol) λ, one of the 15 cellular pols, belongs to the X family. It is a small 575 amino-acid protein containing a polymerase, a dRP-lyase, a proline/serine rich and a BRCT domain. Pol λ shows various enzymatic activities including DNA polymerization, terminal transferase and dRP-lyase. It has been implicated to play a role in several DNA repair pathways, particularly base excision repair (BER), non-homologous end-joining (NHEJ) and translesion DNA synthesis (TLS). Similarly to other DNA repair enzymes, pol λ undergoes posttranslational modifications during the cell cycle that regulate its stability and possibly its subcellular localization. Here we describe our knowledge about ubiquitylation of pol λ and the impact of this modification on its regulation.
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Affiliation(s)
- Enni Markkanen
- Institute for Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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17
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Belousova EA, Lavrik OI. DNA polymerases β and λ and their roles in DNA replication and repair. Mol Biol 2010. [DOI: 10.1134/s0026893310060014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Mizushina Y, Zhang J, Pugliese A, Kim SH, Lü J. Anti-cancer gallotannin penta-O-galloyl-beta-D-glucose is a nanomolar inhibitor of select mammalian DNA polymerases. Biochem Pharmacol 2010; 80:1125-32. [PMID: 20599777 DOI: 10.1016/j.bcp.2010.06.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 06/18/2010] [Accepted: 06/21/2010] [Indexed: 11/16/2022]
Abstract
Penta-1,2,3,4,6-O-galloyl-beta-D-glucose (PGG) has been shown by us and others to inhibit the in vivo growth of human prostate cancer (PCa) xenografts in athymic nude mice and mouse lung cancer allograft in syngenic mice without evident adverse effect on their body weight. We observed a rapid inhibition of DNA synthesis in S-phase cells in PGG-exposed cancer cells and in PGG-treated isolated nuclei. The purpose of the present study was to test the hypothesis that PGG inhibits DNA replicative synthesis through a direct inhibition of one or more DNA polymerases (pols). Using purified pols, we show that PGG exhibited a selective inhibition against the activities of B-family replicative pols (alpha, delta and epsilon) and Y-family (eta, iota and kappa) of bypass synthesis pols, and the inhibitory effect of PGG on pol alpha was the strongest with IC(50) value of 13 nM. PGG also inhibited pol beta, but the potency was an order of magnitude less than against pol alpha. PGG inhibition of pol alpha and kappa activity was non-competitive with respect to the DNA template-primer and the dNTP substrate; whereas it inhibited pol beta competitively. Docking simulation on pol beta, which is the only mammalian pol with solved crystal structure, suggests several favorable interactions with the catalytic pocket/binding site for the incoming dNTP. These results support PGG as a novel inhibitor of select families of mammalian pols by distinct mechanisms, and suggest that the potent pol inhibition may contribute to its anti-cancer efficacy.
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Affiliation(s)
- Yoshiyuki Mizushina
- Laboratory of Food & Nutritional Sciences, Department of Nutritional Science, Kobe-Gakuin University, Kobe, Japan.
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19
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Yamtich J, Sweasy JB. DNA polymerase family X: function, structure, and cellular roles. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:1136-50. [PMID: 19631767 PMCID: PMC2846199 DOI: 10.1016/j.bbapap.2009.07.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/02/2009] [Accepted: 07/03/2009] [Indexed: 10/20/2022]
Abstract
The X family of DNA polymerases in eukaryotic cells consists of terminal transferase and DNA polymerases beta, lambda, and mu. These enzymes have similar structural portraits, yet different biochemical properties, especially in their interactions with DNA. None of these enzymes possesses a proofreading subdomain, and their intrinsic fidelity of DNA synthesis is much lower than that of a polymerase that functions in cellular DNA replication. In this review, we discuss the similarities and differences of three members of Family X: polymerases beta, lambda, and mu. We focus on biochemical mechanisms, structural variation, fidelity and lesion bypass mechanisms, and cellular roles. Remarkably, although these enzymes have similar three-dimensional structures, their biochemical properties and cellular functions differ in important ways that impact cellular function.
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Affiliation(s)
- Jennifer Yamtich
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520
| | - Joann B. Sweasy
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520
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20
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Abstract
The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time.
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21
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Lieber MR, Gu J, Lu H, Shimazaki N, Tsai AG. Nonhomologous DNA end joining (NHEJ) and chromosomal translocations in humans. Subcell Biochem 2010; 50:279-96. [PMID: 20012587 DOI: 10.1007/978-90-481-3471-7_14] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Double-strand breaks (DSBs) arise in dividing cells about ten times per cell per day. Causes include replication across a nick, free radicals of oxidative metabolism, ionizing radiation, and inadvertent action by enzymes of DNA metabolism (such as failures of type II topoisomerases or cleavage by recombinases at off-target sites). There are two major double-strand break repair pathways. Homologous recombination (HR) can repair double-strand breaks, but only during S phase and typically only if there are hundreds of base pairs of homology. The more commonly used pathway is nonhomologous DNA end joining, abbreviated NHEJ. NHEJ can repair a DSB at any time during the cell cycle and does not require any homology, although a few nucleotides of terminal microhomology are often utilized by the NHEJ enzymes, if present. The proteins and enzymes of NHEJ include Ku, DNA-PKcs, Artemis, DNA polymerase mu (Pol micro), DNA polymerase lambda (Pol lambda), XLF (also called Cernunnos), XRCC4, and DNA ligase IV. These enzymes constitute what some call the classical NHEJ pathway, and in wild type cells, the vast majority of joining events appear to proceed using these components. NHEJ is present in many prokaryotes, as well as all eukaryotes, and very similar mechanistic flexibility evolved both convergently and divergently. When two double-strand breaks occur on different chromosomes, then the rejoining is almost always done by NHEJ. The causes of DSBs in lymphomas most often involve the RAG or AID enzymes that function in the specialized processes of antigen receptor gene rearrangement.
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Affiliation(s)
- Michael R Lieber
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA.
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22
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Abstract
Double-strand DNA breaks are common events in eukaryotic cells, and there are two major pathways for repairing them: homologous recombination (HR) and nonhomologous DNA end joining (NHEJ). The various causes of double-strand breaks (DSBs) result in a diverse chemistry of DNA ends that must be repaired. Across NHEJ evolution, the enzymes of the NHEJ pathway exhibit a remarkable degree of structural tolerance in the range of DNA end substrate configurations upon which they can act. In vertebrate cells, the nuclease, DNA polymerases, and ligase of NHEJ are the most mechanistically flexible and multifunctional enzymes in each of their classes. Unlike repair pathways for more defined lesions, NHEJ repair enzymes act iteratively, act in any order, and can function independently of one another at each of the two DNA ends being joined. NHEJ is critical not only for the repair of pathologic DSBs as in chromosomal translocations, but also for the repair of physiologic DSBs created during variable (diversity) joining [V(D)J] recombination and class switch recombination (CSR). Therefore, patients lacking normal NHEJ are not only sensitive to ionizing radiation (IR), but also severely immunodeficient.
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Affiliation(s)
- Michael R Lieber
- Norris Comprehensive Cancer Center, Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, California 90089, USA.
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23
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Brown JA, Fiala KA, Fowler JD, Sherrer SM, Newmister SA, Duym WW, Suo Z. A novel mechanism of sugar selection utilized by a human X-family DNA polymerase. J Mol Biol 2009; 395:282-90. [PMID: 19900463 DOI: 10.1016/j.jmb.2009.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 10/20/2022]
Abstract
During DNA synthesis, most DNA polymerases and reverse transcriptases select against ribonucleotides via a steric clash between the ribose 2'-hydroxyl group and the bulky side chain of an active-site residue. In this study, we demonstrated that human DNA polymerase lambda used a novel sugar selection mechanism to discriminate against ribonucleotides, whereby the ribose 2'-hydroxyl group was excluded mostly by a backbone segment and slightly by the side chain of Y505. Such steric clash was further demonstrated to be dependent on the size and orientation of the substituent covalently attached at the ribonucleotide C2'-position.
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Affiliation(s)
- Jessica A Brown
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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24
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An 8-oxo-guanine repair pathway coordinated by MUTYH glycosylase and DNA polymerase lambda. Proc Natl Acad Sci U S A 2009; 106:18201-6. [PMID: 19820168 DOI: 10.1073/pnas.0907280106] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Reactive oxygen species (ROS) interact with DNA, frequently generating highly mutagenic 7,8-dihydro-8-oxoguanine (8-oxo-G) lesions. Replicative DNA polymerases (pols) often misincorporate adenine opposite 8-oxo-G. The subsequent repair mechanism allowing the removal of adenine and formation of C:8-oxo-G base pair is essential to prevent C:G to A:T transversion mutations. Here, we show by immunofluorescence experiments, in cells exposed to ROS, the involvement of MutY glycosylase homologue (MUTYH) and DNA pol lambda in the repair of A:8-oxo-G mispairs. We observe specific recruitment of MUTYH, DNA pol lambda, proliferating cell nuclear antigen (PCNA), flap endonuclease 1 (FEN1) and DNA ligases I and III from human cell extracts to A:8-oxo-G DNA, but not to undamaged DNA. Using purified human proteins and a DNA template, we reconstitute the full pathway for the faithful repair of A:8-oxo-G mispairs involving MUTYH, DNA pol lambda, FEN1, and DNA ligase I. These results reveal a cellular response pathway to ROS, important to sustain genomic stability and modulate carcinogenesis.
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25
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Romain F, Barbosa I, Gouge J, Rougeon F, Delarue M. Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region. Nucleic Acids Res 2009; 37:4642-56. [PMID: 19502493 PMCID: PMC2724280 DOI: 10.1093/nar/gkp460] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 12/31/2022] Open
Abstract
Terminal deoxynucleotidyltransferase (Tdt) and DNA polymerase mu (pol mu) are two eukaryotic highly similar proteins involved in DNA processing and repair. Despite their high sequence identity, they differ widely in their activity: pol mu has a templated polymerase activity, whereas Tdt has a non-templated one. Loop1, first described when the Tdt structure was solved, has been invoked as the major structural determinant of this difference. Here we describe attempts to transform Tdt into pol mu with the minimal number of mutations in and around Loop1. First we describe the effect of mutations on six different positions chosen to destabilize Tdt Loop1 structure, either by alanine substitution or by deletion; they result at most in a reduction of Tdt activity, but adding Co(++) restores most of this Tdt activity. However, a deletion of the entire Loop1 as in pol lambda does confer a limited template-dependent polymerase behavior to Tdt while a chimera bearing an extended pol mu Loop1 reproduces pol mu behavior. Finally, 16 additional substitutions are reported, targeted at the two so-called 'sequence determinant' regions located just after Loop1 or underneath. Among them, the single-point mutant F401A displays a sequence-specific replicative polymerase phenotype that is stable upon Co(++) addition. These results are discussed in light of the available crystal structures.
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Affiliation(s)
- Félix Romain
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Isabelle Barbosa
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Jérôme Gouge
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - François Rougeon
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
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26
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Ohba T, Kometani T, Shoji F, Yano T, Ichiro Y, Taguchi K, Kuraoka I, Oda S, Maehara Y. Expression of an X-family DNA polymerase, pol lambda, in the respiratory epithelium of non-small cell lung cancer patients with habitual smoking. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2009; 677:66-71. [DOI: 10.1016/j.mrgentox.2009.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 04/23/2009] [Accepted: 05/17/2009] [Indexed: 11/26/2022]
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27
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Nakane S, Nakagawa N, Kuramitsu S, Masui R. Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity. Nucleic Acids Res 2009; 37:2037-52. [PMID: 19211662 PMCID: PMC2665239 DOI: 10.1093/nar/gkp064] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The X-family DNA polymerases (PolXs) comprise a highly conserved DNA polymerase family found in all kingdoms. Mammalian PolXs are known to be involved in several DNA-processing pathways including repair, but the cellular functions of bacterial PolXs are less known. Many bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain at their C-termini in addition to a PolX core (POLXc) domain, and possess 3'-5' exonuclease activity. Although both domains are highly conserved in bacteria, their molecular functions, especially for a PHP domain, are unknown. We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-binding activities. We identified the domains of ttPolX by limited proteolysis and characterized their biochemical activities. The POLXc domain was responsible for the polymerase and DNA-binding activities but exonuclease activity was not detected for either domain. However, the POLXc and PHP domains interacted with each other and a mixture of the two domains had Mn(2+)-dependent 3'-5' exonuclease activity. Moreover, site-directed mutagenesis revealed catalytically important residues in the PHP domain for the 3'-5' exonuclease activity. Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3'-5' exonuclease activity.
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Affiliation(s)
- Shuhei Nakane
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Numt-mediated double-strand break repair mitigates deletions during primate genome evolution. PLoS Genet 2008; 4:e1000237. [PMID: 18949041 PMCID: PMC2567098 DOI: 10.1371/journal.pgen.1000237] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 09/23/2008] [Indexed: 12/21/2022] Open
Abstract
Non-homologous end joining (NHEJ) is the major mechanism of double-strand break repair (DSBR) in mammalian cells. NHEJ has traditionally been inferred from experimental systems involving induced double strand breaks (DSBs). Whether or not the spectrum of repair events observed in experimental NHEJ reflects the repair of natural breaks by NHEJ during chromosomal evolution is an unresolved issue. In primate phylogeny, nuclear DNA sequences of mitochondrial origin, numts, are inserted into naturally occurring chromosomal breaks via NHEJ. Thus, numt integration sites harbor evidence for the mechanisms that act on the genome over evolutionary timescales. We have identified 35 and 55 lineage-specific numts in the human and chimpanzee genomes, respectively, using the rhesus monkey genome as an outgroup. One hundred and fifty two numt-chromosome fusion points were classified based on their repair patterns. Repair involving microhomology and repair leading to nucleotide additions were detected. These repair patterns are within the experimentally determined spectrum of classical NHEJ, suggesting that information from experimental systems is representative of broader genetic loci and end configurations. However, in incompatible DSBR events, small deletions always occur, whereas in 54% of numt integration events examined, no deletions were detected. Numts show a statistically significant reduction in deletion frequency, even in comparison to DSBR involving filler DNA. Therefore, numts show a unique mechanism of integration via NHEJ. Since the deletion frequency during numt insertion is low, native overhangs of chromosome breaks are preserved, allowing us to determine that 24% of the analyzed breaks are cohesive with overhangs of up to 11 bases. These data represent, to the best of our knowledge, the most comprehensive description of the structure of naturally occurring DSBs. We suggest a model in which the sealing of DSBs by numts, and probably by other filler DNA, prevents nuclear processing of DSBs that could result in deleterious repair. Changes to DNA sequence are the major source of variation in evolution. Those changes often arise from damage to DNA that is repaired in a way that fails to restore the original sequence. One type of DNA damage is a chromosomal double-strand break. Such breaks are mostly studied experimentally in model systems, because naturally occurring chromosomal breaks are hard to follow. Here, we used an evolutionary approach to study the repair of naturally occurring chromosomal breaks. Throughout evolutionary history, fragments of the mitochondrial genome, known as numts (nuclear sequences of mitochondrial origin), have been inserted into the nuclear genome. Numts are passively captured into random chromosomal breaks, leaving sequence traces in genomes. Humans and chimpanzees share a recent common ancestor and their genomes share high sequence similarity; therefore, their species-specific numts can be used to follow both some of the break structure and repair mechanisms. Comparing naturally occurring break and repair patterns with experimental repair patterns identified similarities but also highlighted a clear difference. Experimental breaks usually involve deletions, while deletions were significantly less frequent in the numt based repair system. We propose that extra-chromosomal DNA sequences, like numts, play a role in maintaining genome integrity by protecting naturally occurring chromosomal breaks from further deleterious processing.
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Tsuji H, Ishii-Ohba H, Noda Y, Kubo E, Furuse T, Tatsumi K. Rag-dependent and Rag-independent mechanisms of Notch1 rearrangement in thymic lymphomas of Atm(-/-) and scid mice. Mutat Res 2008; 660:22-32. [PMID: 19000702 DOI: 10.1016/j.mrfmmm.2008.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 10/06/2008] [Accepted: 10/07/2008] [Indexed: 11/26/2022]
Abstract
The pathways of thymic lymphomagenesis are classified as Rag-dependent or -independent according to their dependence on recombination-activating gene (Rag1/2) proteins. The role of the two-lymphoma pathways in oncogene rearrangements and the connection between lymphoma pathways and rearrangement mechanisms, however, remain obscure. We compared the incidence and latency of thymic lymphomas, and associated rearrangements of the representative oncogene Notch1 among Rag2(-/-), ataxia telangiectasia mutated (Atm)(-/-), and severe combined immune deficiency (scid) mice combined with Rag2 deficiency. Contrary to expectations, Rag2(-/-) mice were prone to thymic lymphoma development, suggesting the existence of a Rag2-independent lymphoma pathway in Rag2(-/-) mice. The lymphoma incidence in Rag2(-/-)Atm(-/-) mice was lower than that in Atm(-/-) mice, but higher than that in Rag2(-/-) mice, indicating that Atm(-/-) mice develop lymphomas through both pathways. Scid mice developed lymphomas with an incidence and latency similar to Rag2(-/-)scid mice, suggesting that Rag2-mediated V(D)J recombination-driven events are not necessarily required for lymphomagenesis in scid mice. Notch1 rearrangement mechanisms were classified as Rag2-dependent or Rag2-independent based on the presence of recombination signal-like sequences at rearranged sites. In Rag2(-/-) lymphomas, Notch1 must be rearranged independently of Rag2 function, implying that Rag2(-/-) mice are susceptible to lymphomagenesis due to the presence of other rearrangement mechanisms. The results in Atm(-/-) mice suggest that Notch1 was rearranged through both lymphoma pathways. In scid mice, the frequency of Rag2-mediated rearrangements was relatively low compared with that in wild-type mice, suggesting that the Rag2-independent lymphoma pathway prevails in the development of thymic lymphomas in scid mice. Thus, two rearrangement mechanisms underlie the lymphoma pathways and constitute the mechanistic bases for lymphomagenesis, thereby providing the molecular criteria for distinguishing between Rag2-dependent and Rag2-independent lymphoma pathways.
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Affiliation(s)
- Hideo Tsuji
- Research Center for Radiation Protection, National Institute of Radiological Sciences, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan.
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Characterization of a Bacillus subtilis 64-kDa DNA polymerase X potentially involved in DNA repair. J Mol Biol 2008; 384:1019-28. [PMID: 18938175 DOI: 10.1016/j.jmb.2008.09.081] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 09/18/2008] [Accepted: 09/26/2008] [Indexed: 11/20/2022]
Abstract
Bacillus subtilis gene yshC encodes a 64-kDa family X DNA polymerase (PolXBs), which contains all the critical residues involved in DNA and nucleotide binding as well as those responsible for catalysis of DNA polymerization, conserved in most family X members. Biochemical analyses of the purified enzyme indicate that PolXBs is a monomeric and strictly template-directed DNA polymerase, preferentially acting on DNA structures containing gaps from one to a few nucleotides and bearing a phosphate group at the 5' end of the downstream DNA. The fact that PolXBs is able to conduct filling of a single-nucleotide gap, allowing further sealing of the resulting nick by a DNA ligase, points to a putative role in base excision repair during the B. subtilis life cycle.
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Prato S, Vitale RM, Contursi P, Lipps G, Saviano M, Rossi M, Bartolucci S. Molecular modeling and functional characterization of the monomeric primase-polymerase domain from the Sulfolobus solfataricus plasmid pIT3. FEBS J 2008; 275:4389-402. [PMID: 18671730 DOI: 10.1111/j.1742-4658.2008.06585.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A tri-functional monomeric primase-polymerase domain encoded by the plasmid pIT3 from Sulfolobus solfataricus strain IT3 was identified using a structural-functional approach. The N-terminal domain of the pIT3 replication protein encompassing residues 31-245 (i.e. Rep245) was modeled onto the crystallographic structure of the bifunctional primase-polymerase domain of the archaeal plasmid pRN1 and refined by molecular dynamics in solution. The Rep245 protein was purified following overexpression in Escherichia coli and its nucleic acid synthesis activity was characterized. The biochemical properties of the polymerase activity such as pH, temperature optima and divalent cation metal dependence were described. Rep245 was capable of utilizing both ribonucleotides and deoxyribonucleotides for de novo primer synthesis and it synthesized DNA products up to several kb in length in a template-dependent manner. Interestingly, the Rep245 primase-polymerase domain harbors also a terminal nucleotidyl transferase activity, being able to elongate the 3'-end of synthetic oligonucleotides in a non-templated manner. Comparative sequence-structural analysis of the modeled Rep245 domain with other archaeal primase-polymerases revealed some distinctive features that could account for the multifaceted activities exhibited by this domain. To the best of our knowledge, Rep245 typifies the shortest functional domain from a crenarchaeal plasmid endowed with DNA and RNA synthesis and terminal transferase activity.
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Affiliation(s)
- Santina Prato
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli Federico II, Naples, Italy
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Le Breton M, Henneke G, Norais C, Flament D, Myllykallio H, Querellou J, Raffin JP. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair? J Mol Biol 2007; 374:1172-85. [PMID: 17991487 DOI: 10.1016/j.jmb.2007.10.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 11/27/2022]
Abstract
We report on the characterization of the DNA primase complex of the hyperthermophilic archaeon Pyrococcus abyssi (Pab). The Pab DNA primase complex is composed of the proteins Pabp41 and Pabp46, which show sequence similarities to the p49 and p58 subunits, respectively, of the eukaryotic polymerase alpha-primase complex. Both subunits were expressed, purified, and characterized. The Pabp41 subunit alone had no RNA synthesis activity but could synthesize long (up to 3 kb) DNA strands. Addition of the Pabp46 subunit increased the rate of DNA synthesis but decreased the length of the DNA fragments synthesized and conferred RNA synthesis capability. Moreover, in our experimental conditions, Pab DNA primase had comparable affinities for ribonucleotides and deoxyribonucleotides, and its activity was dependent on the presence of Mg2+ and Mn2+. Interestingly, Pab DNA primase also displayed DNA polymerase, gap-filling, and strand-displacement activities. Genetic analyses undertaken in Haloferax volcanii suggested that the eukaryotic-type heterodimeric primase is essential for survival in archaeal cells. Our results are in favor of a multifunctional archaeal primase involved in priming and repair.
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Affiliation(s)
- Magali Le Breton
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Ifremer, BP 70, F-29280 Plouzané, France
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Gu F, You C, Liu J, Chen A, Yu Y, Wang X, Wan D, Gu J, Yuan H, Li Y, Lü H. Cloning, expression and characterization of human tissue-specific DNA polymerase λ2. ACTA ACUST UNITED AC 2007; 50:457-65. [PMID: 17653665 DOI: 10.1007/s11427-007-0059-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
DNA polymerase (POL) lambda plays an important role during DNA repair and DNA nonhomologous recombination processes. A novel POL lambda variant was cloned from a human liver cDNA library and named POL lambda2 (GenBank Accession No. AY302442). POL lambda2 has 2206 base pairs in length with an open reading frame of 1452 base pairs encoding a 482-amino-acids protein. Bioinformatics analysis reveals that POL lambda2 spans 7.9 kb on human chromosome 10q24 and is composed of 8 exons and 7 introns. It has the specific domain of DNA polymerase X family-POL Xc at the C-terminus and BRCT domain at the N-terminus. POL lambda2 was localized predominantly in nucleus in transfected L0-2 cells. It was expressed abundantly in liver and testis, weakly in ovary, and undetectably in other tested human tissues. In comparison with the expression ratio between POL lambda and POL lambda2 in normal liver tissues and hepatocellular carcinoma (HCC) adjacent tissues, the ratio was aberrant in 80% of those 15 HCC specimens examined due to the up-regulated expression of POL lambda. This abnormality might be involved in hepatocarcinogenesis. The recombinant POL lambda2 with His-tag was expressed as a soluble active protein in E. coli BL21 (DE3)CONDON Plus and purified by Ni-NTA resin and then desalted by Superdex-75 chromatography in an FPLC system. The analysis using isotope a-(32)P-dCTP incorporation in vitro showed that the purified recombinant POL lambda2 exhibited DNA polymerase activity.
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Affiliation(s)
- Fu Gu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
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Gu J, Lu H, Tippin B, Shimazaki N, Goodman MF, Lieber MR. XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps. EMBO J 2007; 26:1010-23. [PMID: 17290226 PMCID: PMC1852838 DOI: 10.1038/sj.emboj.7601559] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 12/19/2006] [Indexed: 11/08/2022] Open
Abstract
XRCC4 and DNA ligase IV form a complex that is essential for the repair of all double-strand DNA breaks by the nonhomologous DNA end joining pathway in eukaryotes. We find here that human XRCC4:DNA ligase IV can ligate two double-strand DNA ends that have fully incompatible short 3' overhang configurations with no potential for base pairing. Moreover, at DNA ends that share 1-4 annealed base pairs, XRCC4:DNA ligase IV can ligate across gaps of 1 nt. Ku can stimulate the joining, but is not essential when there is some terminal annealing. Polymerase mu can add nucleotides in a template-independent manner under physiological conditions; and the subset of ends that thereby gain some terminal microhomology can then be ligated. Hence, annealing at sites of microhomology is very important, but the flexibility of the ligase complex is paramount in nonhomologous DNA end joining. These observations provide an explanation for several in vivo observations that were difficult to understand previously.
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Affiliation(s)
- Jiafeng Gu
- Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, and Biological Sciences, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- Department of Biological Sciences, Los Angeles, CA, USA
| | - Haihui Lu
- Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, and Biological Sciences, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | - Noriko Shimazaki
- Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, and Biological Sciences, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | - Michael R Lieber
- Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, and Biological Sciences, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- Department of Biological Sciences, Los Angeles, CA, USA
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35
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Ishimaru C, Kuriyama I, Shimazaki N, Koiwai O, Sakaguchi K, Kato I, Yoshida H, Mizushina Y. Cholesterol hemisuccinate: a selective inhibitor of family X DNA polymerases. Biochem Biophys Res Commun 2007; 354:619-25. [PMID: 17241613 DOI: 10.1016/j.bbrc.2007.01.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 01/09/2007] [Indexed: 11/26/2022]
Abstract
Cholesterol hemisuccinate (compound 5), which consists of succinic acid esterified to the beta-hydroxyl group of cholesterol, selectively and strongly inhibited the activities of mammalian DNA polymerases (pols) such as pol beta, pol lambda, and terminal deoxynucleotidyltransferase (TdT), which are family X pols, in vitro, and the IC50 values were 2.9, 6.3, and 6.5 microM, respectively. The compound moderately suppressed the activities of other mammalian pols such as pol A (i.e., pol gamma), pol B (i.e., pols alpha, delta, and epsilon), and pol Y (i.e., pols iota, eta, and kappa) with 50% inhibition observed at concentrations of 131, 89.2-98.0, and 120-125 microM, respectively. The compound had no influence on the activities of plant pols alpha and beta, prokaryotic pols and other DNA metabolic enzymes tested. Since other cholesterol-related compounds such as cholesterol, cholesteryl chloride, cholesteryl bromide, cholesteryl acetate, and cholesteryl-5alpha, 6alpha-epoxide (compounds 1-4 and 6, respectively) did not influence the activities of any enzymes tested, the hemisuccinate group of compound 5 could be important for inhibition of the pol X family. Surface plasmon resonance analysis demonstrated that compound 5 bound selectively to the C-terminal 31 kDa domain of pol beta and pol lambda containing a pol beta-like region. On the basis of these results, the inhibitory mechanism of compound 5 on the pol X family was discussed.
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Affiliation(s)
- Chisato Ishimaru
- Laboratory of Food & Nutritional Sciences, Department of Nutritional Science, Kobe-Gakuin University, Kobe, Hyogo 651-2180, Japan
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36
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De Falco M, Ferrari E, De Felice M, Rossi M, Hübscher U, Pisani FM. The human GINS complex binds to and specifically stimulates human DNA polymerase alpha-primase. EMBO Rep 2006; 8:99-103. [PMID: 17170760 PMCID: PMC1796748 DOI: 10.1038/sj.embor.7400870] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 10/09/2006] [Accepted: 11/06/2006] [Indexed: 11/09/2022] Open
Abstract
The eukaryotic GINS complex has an essential role in the initiation and elongation phases of genome duplication. It is composed of four paralogous subunits--Sld5, Psf1, Psf2 and Psf3--which are ubiquitous and evolutionarily conserved in eukaryotic organisms. Here, we report the biochemical characterization of the human GINS complex (hGINS). The four hGINS subunits were coexpressed in Escherichia coli in a highly soluble form and purified as a complex. hGINS was shown to interact directly with the heterodimeric human DNA primase, by using either surface plasmon resonance measurements or by immunoprecipitation experiments carried out with anti-hGINS antibodies. The DNA polymerase alpha-primase synthetic activity was specifically stimulated by hGINS on various primed DNA templates. The significance of these findings is discussed in view of the molecular dynamics at the human replication fork.
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Affiliation(s)
- Mariarosaria De Falco
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, Napoli 80131, Italy
| | - Elena Ferrari
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Winterthurerstrasse 190, Zürich CH 8057, Switzerland
| | - Mariarita De Felice
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, Napoli 80131, Italy
| | - Mosè Rossi
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, Napoli 80131, Italy
| | - Ulrich Hübscher
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Winterthurerstrasse 190, Zürich CH 8057, Switzerland
| | - Francesca M Pisani
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, Napoli 80131, Italy
- Tel: +39 0816132292; Fax: +39 0816132277; E-mail:
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Murray JM, O’Neill JP, Messier T, Rivers J, Walker VE, McGonagle B, Trombley L, Cowell LG, Kelsoe G, McBlane F, Finette BA. V(D)J recombinase-mediated processing of coding junctions at cryptic recombination signal sequences in peripheral T cells during human development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2006; 177:5393-404. [PMID: 17015725 PMCID: PMC1937029 DOI: 10.4049/jimmunol.177.8.5393] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
V(D)J recombinase mediates rearrangements at immune loci and cryptic recombination signal sequences (cRSS), resulting in a variety of genomic rearrangements in normal lymphocytes and leukemic cells from children and adults. The frequency at which these rearrangements occur and their potential pathologic consequences are developmentally dependent. To gain insight into V(D)J recombinase-mediated events during human development, we investigated 265 coding junctions associated with cRSS sites at the hypoxanthine-guanine phosphoribosyltransferase (HPRT) locus in peripheral T cells from 111 children during the late stages of fetal development through early adolescence. We observed a number of specific V(D)J recombinase processing features that were both age and gender dependent. In particular, TdT-mediated nucleotide insertions varied depending on age and gender, including percentage of coding junctions containing N-nucleotide inserts, predominance of GC nucleotides, and presence of inverted repeats (Pr-nucleotides) at processed coding ends. In addition, the extent of exonucleolytic processing of coding ends was inversely related to age. We also observed a coding-partner-dependent difference in exonucleolytic processing and an age-specific difference in the subtypes of V(D)J-mediated events. We investigated these age- and gender-specific differences with recombination signal information content analysis of the cRSS sites in the human HPRT locus to gain insight into the mechanisms mediating these developmentally specific V(D)J recombinase-mediated rearrangements in humans.
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Affiliation(s)
- Janet M. Murray
- Department of Pediatrics, University of Vermont, Burlington, VT 05405
| | - J. Patrick O’Neill
- Department of Pediatrics, University of Vermont, Burlington, VT 05405
- Vermont Cancer Center, University of Vermont, Burlington, VT 05405
| | - Terri Messier
- Department of Pediatrics, University of Vermont, Burlington, VT 05405
- Vermont Cancer Center, University of Vermont, Burlington, VT 05405
| | - Jami Rivers
- Department of Pediatrics, University of Vermont, Burlington, VT 05405
- Vermont Cancer Center, University of Vermont, Burlington, VT 05405
| | | | | | - Lucy Trombley
- Vermont Cancer Center, University of Vermont, Burlington, VT 05405
| | - Lindsay G. Cowell
- Division of Computational Biology, Department of Biostatistics and Bioinformatics, and
| | - Garnett Kelsoe
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Fraser McBlane
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Barry A. Finette
- Department of Pediatrics, University of Vermont, Burlington, VT 05405
- Vermont Cancer Center, University of Vermont, Burlington, VT 05405
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405
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Lieber MR, Yu K, Raghavan SC. Roles of nonhomologous DNA end joining, V(D)J recombination, and class switch recombination in chromosomal translocations. DNA Repair (Amst) 2006; 5:1234-45. [PMID: 16793349 DOI: 10.1016/j.dnarep.2006.05.013] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
When a single double-strand break arises in the genome, nonhomologous DNA end joining (NHEJ) is a major pathway for its repair. When double-strand breaks arise at two nonhomologous sites in the genome, NHEJ also appears to be a major pathway by which the translocated ends are joined. The mechanism of NHEJ is briefly summarized, and alternative enzymes are also discussed. V(D)J recombination and class switch recombination are specialized processes designed to create double-strand DNA breaks at specific locations in the genomes of lymphoid cells. Sporadic Burkitt's lymphoma and myelomas can arise due to translocation of the c-myc gene into the Ig heavy chain locus during class switch recombination. In other lymphoid neoplasms, the RAG complex can create double-strand breaks that result in a translocation. Such RAG-generated breaks occur at very specific nucleotides that are directly adjacent to sequences that resemble canonical heptamer/nonamer sequences characteristic of normal V(D)J recombination. This occurs in some T cell leukemias and lymphomas. The RAG complex also appears capable of recognizing regions for their altered DNA structure rather than their primary sequence, and this may account for the action by RAGs at some chromosomal translocation sites, such as at the bcl-2 major breakpoint region in the follicular lymphomas that arise in B lymphocytes.
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Affiliation(s)
- Michael R Lieber
- USC Norris Comprehensive Cancer Ctr., Rm. 5428, University of Southern California, Keck School of Medicine 1441 Eastlake Ave, MC 9176 Los Angeles, CA 90089, USA.
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40
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Krutyakov VM. Eukaryotic error-prone DNA polymerases: The presumed roles in replication, repair, and mutagenesis. Mol Biol 2006. [DOI: 10.1134/s0026893306010018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Locatelli G, Savio M, Forti L, Shevelev I, Ramadan K, Stivala L, Vannini V, Hübscher U, Spadari S, Maga G. Inhibition of mammalian DNA polymerases by resveratrol: mechanism and structural determinants. Biochem J 2005; 389:259-68. [PMID: 15773817 PMCID: PMC1175102 DOI: 10.1042/bj20050094] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Resveratrol, a natural compound found in many dietary plants and in red wine, plays an important role in the prevention of many human pathological processes, including inflammation, atherosclerosis and carcinogenesis. We have shown that the antiproliferative activity of resveratrol correlated with its ability to inhibit the replicative pols (DNA polymerases) alpha and delta in vitro [Stivala, Savio, Carafoli, Perucca, Bianchi, Maga, Forti, Pagnoni, Albini, Prosperi and Vannini (2001) J. Biol. Chem. 276, 22586-22594]. In this paper, we present the first detailed biochemical investigation on the mechanism of action of resveratrol towards mammalian pols. Our results suggest that specific structural determinants of the resveratrol molecule are responsible for selective inhibition of different mammalian pols, such as the family B pol alpha and the family X pol lambda. Moreover, the resveratrol derivative trans-3,5-dimethoxy-4-hydroxystilbene, which is endowed with a strong antiproliferative activity (Stivala et al., 2001), can inhibit pols alpha and lambda and also suppress the in vitro SV40 DNA replication. The potency of inhibition is similar to that of aphidicolin, an inhibitor of the three replicative pols alpha, delta and epsilon. Our findings establish the necessary background for the synthesis of resveratrol derivatives having more selective and potent antiproliferative activity.
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Affiliation(s)
| | - Monica Savio
- †Dipartimento di Medicina Sperimentale, Sez. Patologia Generale, Universita' di Pavia, 27100 Pavia, Italy
| | - Luca Forti
- ‡Dipartimento di Chimica, Università di Modena e Reggio Emilia, 41100 Modena, Italy
| | - Igor Shevelev
- §Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, CH8057 Zürich, Switzerland
| | - Kristijan Ramadan
- §Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, CH8057 Zürich, Switzerland
| | - Lucia A. Stivala
- †Dipartimento di Medicina Sperimentale, Sez. Patologia Generale, Universita' di Pavia, 27100 Pavia, Italy
| | - Vanio Vannini
- †Dipartimento di Medicina Sperimentale, Sez. Patologia Generale, Universita' di Pavia, 27100 Pavia, Italy
| | - Ulrich Hübscher
- §Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, CH8057 Zürich, Switzerland
| | - Silvio Spadari
- *Istituto di Genetica Molecolare IGM-CNR, 27100 Pavia, Italy
- ∥European Research Centre for Drug Discovery and Development (NatSynDrugs), Universita' di Siena, 53100 Siena, Italy
| | - Giovanni Maga
- *Istituto di Genetica Molecolare IGM-CNR, 27100 Pavia, Italy
- ∥European Research Centre for Drug Discovery and Development (NatSynDrugs), Universita' di Siena, 53100 Siena, Italy
- To whom correspondence should be addressed (email )
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42
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Mizushina Y, Yagita E, Kuramochi K, Kuriyama I, Shimazaki N, Koiwai O, Uchiyama Y, Yomezawa Y, Sugawara F, Kobayashi S, Sakaguchi K, Yoshida H. 5-(Hydroxymethyl)-2-furfural: a selective inhibitor of DNA polymerase lambda and terminal deoxynucleotidyltransferase. Arch Biochem Biophys 2005; 446:69-76. [PMID: 16405901 DOI: 10.1016/j.abb.2005.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 11/24/2005] [Accepted: 11/29/2005] [Indexed: 11/23/2022]
Abstract
5-(Hydroxymethyl)-2-furfural (HMF), a pyrolysate of carbohydrate isolated from instant coffee (Coffea arabica L.), selectively inhibits the activities of mammalian DNA polymerase lambda (pol lambda) and terminal deoxynucleotidyltransferase (TdT) which are family X pols, in vitro. The compound influenced neither the activities of replicative DNA polymerases such as alpha, delta, and epsilon, nor even the activity of pol beta which is from the same family and thought to have a very similar three-dimensional structure to the pol beta-like region of pol lambda. Since parts of HMF such as furan, furfuryl alcohol, and 2-furaldehyde did not influence the activities of any enzymes tested, the substituted form of furan with a hyroxymethyl group and a formyl group might be important for the inhibition of pol lambda and TdT. The inhibitory effect of HMF on intact pol lambda (i.e., residues 1-575), a truncated pol lambda lacking the N-terminal BRCA1 C-terminus domain (133-575, del-1 pol lambda) and another truncated pol lambda lacking the N-terminal proline-rich region (245-575, del-2 pol lambda) was dose-dependent, and 50% inhibition was observed at a concentration of 26.1, 10.3, and 4.6 microM, respectively. The IC(50) value of HMF for TdT was the same as that for del-2 pol lambda (5.5 microM). The HMF-induced inhibition of both pol lambda and TdT activities was competitive with respect to both the DNA template-primer and the dNTP substrate. On the basis of these results, HMF was suggested to bind to the pol beta-like region of pol lambda and TdT.
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Affiliation(s)
- Yoshiyuki Mizushina
- Laboratory of Food and Nutritional Sciences, Department of Nutritional Science, Kobe-Gakuin University, Nishi-ku, Kobe, Hyogo 651-2180, Japan.
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43
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Garcia-Diaz M, Bebenek K, Gao G, Pedersen LC, London RE, Kunkel TA. Structure–function studies of DNA polymerase lambda. DNA Repair (Amst) 2005; 4:1358-67. [PMID: 16213194 DOI: 10.1016/j.dnarep.2005.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA polymerase lambda is a member of the X family of polymerases that is implicated in non-homologous end-joining of double-strand breaks in DNA and in base excision repair of DNA damage. To better understand the roles of DNA polymerase lambda in these repair pathways, here we review its structure and biochemical properties, with emphasis on its gap-filling polymerization activity, its dRP lyase activity and its unusual DNA synthetic (in)fidelity.
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Affiliation(s)
- Miguel Garcia-Diaz
- Laboratory of Structural Biology and Laboratory of Molecular Genetics NIEHS, NIH, DHHS, Research Triangle Park, NC 27709, USA
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44
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Lebedeva NA, Rechkunova NI, Dezhurov SV, Khodyreva SN, Favre A, Blanco L, Lavrik OI. Comparison of functional properties of mammalian DNA polymerase lambda and DNA polymerase beta in reactions of DNA synthesis related to DNA repair. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1751:150-8. [PMID: 15979954 DOI: 10.1016/j.bbapap.2005.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Revised: 05/24/2005] [Accepted: 05/24/2005] [Indexed: 11/22/2022]
Abstract
DNA polymerase lambda (Pol lambda) is a novel enzyme of the family X of DNA polymerases. Pol lambda has some properties in common with DNA polymerase beta (Pol beta). The substrate properties of Pol lambda were compared to Pol beta using DNAs mimicking short-patch (SP) and long-patch (LP) base excision repair (BER) intermediates as well as recessed template primers. In the present work, the influence of several BER proteins such as flap-endonuclease-1 (FEN1), PCNA, and apurinic/apyrimidinic endonuclease-1 (APE1) on the activity of Pol lambda was investigated. Pol lambda is unable to catalyze strand displacement synthesis using nicked DNA, although this enzyme efficiently incorporates a dNMP into a one-nucleotide gap. FEN1 and PCNA stimulate the strand displacement activity of Pol lambda. FEN1 processes nicked DNA, thus removing a barrier to Pol lambda DNA synthesis. It results in a one-nucleotide gapped DNA molecule that is a favorite substrate of Pol lambda. Photocrosslinking and functional assay show that Pol lambda is less efficient than Pol beta in binding to nicked DNA. APE1 has no influence on the strand displacement activity of Pol lambda though it stimulates strand displacement synthesis catalyzed with Pol beta. It is suggested that Pol lambda plays a role in the SP BER rather than contributes to the LP BER pathway.
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Affiliation(s)
- Natalia A Lebedeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, pr. Lavrentieva 8, 630090, Novosibirsk, Russia
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45
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Frouin I, Toueille M, Ferrari E, Shevelev I, Hübscher U. Phosphorylation of human DNA polymerase lambda by the cyclin-dependent kinase Cdk2/cyclin A complex is modulated by its association with proliferating cell nuclear antigen. Nucleic Acids Res 2005; 33:5354-61. [PMID: 16174846 PMCID: PMC1226315 DOI: 10.1093/nar/gki845] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA polymerase (Pol) lambda is a member of the Pol X family and possesses four different enzymatic activities, being DNA polymerase, terminal transferase, deoxyribose phosphate lyase and polynucleotide synthetase, all localized in its C-terminal region. On the basis of its biochemical properties, Pol lambda has been implicated in various DNA repair pathways, such as abasic site translesion DNA synthesis, base excision repair and non-homologous end joining of double strand breaks. However, its role in vivo has not yet been elucidated. In addition, Pol lambda has been shown to interact with the replication clamp proliferating cell nuclear antigen (PCNA) in vitro and in vivo. In this work, we searched by affinity chromatography for novel partners and we identified the cyclin-dependent kinase Cdk2 as novel partner of Pol lambda. Pol lambda is phosphorylated in vitro by several Cdk/cyclin complexes, including Cdk2/cyclin A, in its proline-serine-rich domain. While the polymerase activity of Pol lambda was not affected by Cdk2/cyclin A phosphorylation, phosphorylation of Pol lambda was decreased by its interaction with PCNA. Finally, Pol lambda is also phosphorylated in vivo in human cells and this phosphorylation is modulated during the cell cycle.
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Affiliation(s)
| | | | | | | | - Ulrich Hübscher
- To whom correspondence should be addressed. Tel: + 41 16 35 54 72/71; Fax: +41 16 35 68 40;
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46
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Daley JM, Laan RLV, Suresh A, Wilson TE. DNA Joint Dependence of Pol X Family Polymerase Action in Nonhomologous End Joining. J Biol Chem 2005; 280:29030-7. [PMID: 15964833 DOI: 10.1074/jbc.m505277200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA double strand breaks (DSBs) can be rejoined directly by the nonhomologous end-joining (NHEJ) pathway of repair. Nucleases and polymerases are required to promote accurate NHEJ when the terminal bases of the DSB are damaged. The same enzymes also participate in imprecise rejoining and joining of incompatible ends, important mutagenic events. Previous work has shown that the Pol X family polymerase Pol4 is required for some but not all NHEJ events that require gap filling in Saccharomyces cerevisiae. Here, we systematically analyzed DSB end configurations and found that gaps on both strands and overhang polarity are the principal factors that determine whether a joint requires Pol4. DSBs with 3'-overhangs and a gap on each strand strongly depended on Pol4 for repair, DSBs with 5'-overhangs of the same sequence did not. Pol4 was not required when 3'-overhangs contained a gap on only one strand, however. Pol4 was equally required at 3'-overhangs of all lengths within the NHEJ-dependent range but was dispensable outside of this range, indicating that Pol4 is specific to NHEJ. Loss of Pol4 did not affect the rejoining of DSBs that utilized a recessed microhomology or DSBs bearing 5'-hydroxyls but no gap. Finally, mammalian Pol X polymerases were able to differentially complement a pol4 mutation depending on the joint structure, demonstrating that these polymerases can participate in yeast NHEJ but with distinct properties.
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Affiliation(s)
- James M Daley
- Graduate Program in Cellular and Molecular Biology and Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-0602, USA
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47
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Locatelli GA, Di Santo R, Crespan E, Costi R, Roux A, Hübscher U, Shevelev I, Blanca G, Villani G, Spadari S, Maga G. Diketo hexenoic acid derivatives are novel selective non-nucleoside inhibitors of mammalian terminal deoxynucleotidyl transferases, with potent cytotoxic effect against leukemic cells. Mol Pharmacol 2005; 68:538-50. [PMID: 15901847 DOI: 10.1124/mol.105.013326] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mammalian terminal deoxyribonucleotidyl transferase (TDT) catalyzes the non-template-directed polymerization of deoxyribonucleoside triphosphates and has a key role in V(D)J recombination during lymphocyte and repertoire development. More than 90% of leukemic cells in acute lymphocytic leukemia and approximately 30% of leukemic cells in the chronic myelogenous leukemia crisis show elevated TDT activity. This finding is connected to a poor prognosis and response to chemotherapy and reduced survival time. On the other hand, recent data indicated that TDT is not the only terminal deoxyribonucleotidyl transferase in mammalian cells. Its close relative, DNA polymerase lambda, can synthesize DNA both in a template-dependent (polymerase) and template-independent (terminal deoxyribonucleotidyl transferase) fashion. DNA polymerase lambda might be involved in the nonhomologous end-joining recombinational repair pathway of DNA double-strand breaks. In this work, we report the characterization of the mechanism of action of three diketo hexenoic acid (DKHA) derivatives, which proved to be extremely selective for the terminal deoxyribonucleotidyl transferase activity of DNA polymerase lambda and TDT. They seem to be the first non-nucleoside-specific inhibitors of mammalian terminal transferases reported. Moreover, the DKHA analog 6-(1-phenylmethyl-1H-indol-3-yl)-2,4-dioxo-5-hexenoic acid (RDS2119) was not toxic toward HeLa cells (CC(50) > 100 muM), whereas it showed significant cytotoxicity against the TDT(+) leukemia cell line MOLT-4 (CC(50) = 14.9 muM), thus having the potential to be further developed as a novel antitumor agent.
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Affiliation(s)
- Giada A Locatelli
- Istituto di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
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48
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Rebuzzini P, Khoriauli L, Azzalin CM, Magnani E, Mondello C, Giulotto E. New mammalian cellular systems to study mutations introduced at the break site by non-homologous end-joining. DNA Repair (Amst) 2005; 4:546-55. [PMID: 15811627 DOI: 10.1016/j.dnarep.2004.12.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Accepted: 12/27/2004] [Indexed: 01/03/2023]
Abstract
The non-homologous end-joining (NHEJ) pathway is a mechanism to repair DNA double strand breaks, which can introduce mutations at repair sites. We constructed new cellular systems to specifically analyze sequence modifications occurring at the repair site. In particular, we looked for the presence of telomeric repeats at the repair junctions, since our previous work indicated that telomeric sequences could be inserted at break sites in germ-line cells during primate evolution. To induce specific DNA breaks, we used the I-SceI system of Saccharomyces cerevisiae or digestion with restriction enzymes. We isolated human and hamster cell lines containing the I-SceI target site integrated in a single chromosomal locus and we exposed the cells to a continuous expression of the I-SceI endonuclease gene. Additionally, we isolated human cell lines that expressed constitutively the I-SceI endonuclease and we introduced the target site on an episomal plasmid stably transfected into the cells. These strategies allowed us to recover repair junctions in which the I-SceI target site was modified at high frequency (100% in hamster cells and about 70% in human cells). Finally, we analyzed junctions produced on an episomal plasmid linearized by restriction enzymes. In all the systems studied, sequence analysis of individual repair junctions showed that deletions were the most frequent modifications, being present in more than 80% of the junctions. On the episomal plasmids, the average deletion length was greater than at intrachromosomal sites. Insertions of nucleotides or deletions associated with insertions were rare events. Junction organization suggested different mechanisms of formation. To check for the insertion of telomeric sequences, we screened plasmid libraries representing about 3.5 x 10(5) junctions with a telomeric repeat probe. No positive clones were detected, suggesting that the addition of telomeric sequences during double strand break repair in somatic cells in culture is either a very rare event or does not occur at all.
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Affiliation(s)
- Paola Rebuzzini
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy
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49
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Boudsocq F, Benaim P, Canitrot Y, Knibiehler M, Ausseil F, Capp JP, Bieth A, Long C, David B, Shevelev I, Frierich-Heinecken E, Hübscher U, Amalric F, Massiot G, Hoffmann JS, Cazaux C. Modulation of cellular response to cisplatin by a novel inhibitor of DNA polymerase beta. Mol Pharmacol 2005; 67:1485-92. [PMID: 15703384 DOI: 10.1124/mol.104.001776] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA polymerase beta (Pol beta) is an error-prone enzyme whose up-regulation has been shown to be a genetic instability enhancer as well as a contributor to cisplatin resistance in tumor cells. In this work, we describe the isolation of new Pol beta inhibitors after high throughput screening of 8448 semipurified natural extracts. In vitro, the selected molecules affect specifically Pol beta-mediated DNA synthesis compared with replicative extracts from cell nuclei. One of them, masticadienonic acid (MA), is particularly attractive because it perturbs neither the activity of the purified replicative Pol delta nor that of nuclear HeLa cell extracts. With an IC50 value of 8 microM, MA is the most potent of the Pol beta inhibitors found so far. Docking simulation revealed that this molecule could substitute for single-strand DNA in the binding site of Pol beta by binding Lys35, Lys68, and Lys60, which are the main residues involved in the interaction Pol beta/single-strand DNA. Selected inhibitors also affect the Pol beta-mediated translesion synthesis (TLS) across cisplatin adducts; MA was still the most efficient. Therefore, masticadienonic acid sensitized the cisplatin-resistant 2008C13*5.25 human tumor cells. Our data suggest that molecules such as masticadienonic acid could be suitable in conjunction with cisplatin to enhance anticancer treatments.
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Affiliation(s)
- F Boudsocq
- Equipe Instabilité Génétique et Cancer, Institut de Pharmacologie et de Biologie Structurale, Unité Mixte Recherche Centre National de la Recherche Scientifique 5089, Toulouse, France
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50
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Braithwaite EK, Prasad R, Shock DD, Hou EW, Beard WA, Wilson SH. DNA Polymerase λ Mediates a Back-up Base Excision Repair Activity in Extracts of Mouse Embryonic Fibroblasts. J Biol Chem 2005; 280:18469-75. [PMID: 15749700 DOI: 10.1074/jbc.m411864200] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian DNA polymerase (pol) lambda is a member of the X-family of DNA polymerases and has striking enzymatic and structural similarities to mammalian DNA pol beta. Because pol beta provides two important enzymatic activities for base excision repair (BER), we examined whether pol lambda might also contribute to BER. We used extracts from mouse embryonic fibroblasts representing wild-type and null genotypes for pol beta and pol lambda. In combination with neutralizing antibodies against pol beta and pol lambda, our results show a BER deficiency in the pol lambda -/- cell extract compared with extract from isogenic wild-type cells. In addition, the pol lambda antibody strongly reduced in vitro BER in the pol beta -/- cell extract. These data indicate that pol lambda is able to contribute to BER in mouse fibroblast cell extract.
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Affiliation(s)
- Elena K Braithwaite
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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