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Kaminski AM, Pryor JM, Ramsden DA, Kunkel TA, Pedersen LC, Bebenek K. Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break. Nat Commun 2020; 11:4784. [PMID: 32963245 PMCID: PMC7508851 DOI: 10.1038/s41467-020-18506-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/17/2020] [Indexed: 01/07/2023] Open
Abstract
Genomic integrity is threatened by cytotoxic DNA double-strand breaks (DSBs), which must be resolved efficiently to prevent sequence loss, chromosomal rearrangements/translocations, or cell death. Polymerase μ (Polμ) participates in DSB repair via the nonhomologous end-joining (NHEJ) pathway, by filling small sequence gaps in broken ends to create substrates ultimately ligatable by DNA Ligase IV. Here we present structures of human Polμ engaging a DSB substrate. Synapsis is mediated solely by Polμ, facilitated by single-nucleotide homology at the break site, wherein both ends of the discontinuous template strand are stabilized by a hydrogen bonding network. The active site in the quaternary Pol μ complex is poised for catalysis and nucleotide incoporation proceeds in crystallo. These structures demonstrate that Polμ may address complementary DSB substrates during NHEJ in a manner indistinguishable from single-strand breaks.
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Affiliation(s)
- Andrea M. Kaminski
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
| | - John M. Pryor
- grid.10698.360000000122483208Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 32-046 Lineberger Comprehensive Cancer Center, 450 West Dr., CB 7295, Chapel Hill, NC 27599 USA
| | - Dale A. Ramsden
- grid.10698.360000000122483208Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 32-046 Lineberger Comprehensive Cancer Center, 450 West Dr., CB 7295, Chapel Hill, NC 27599 USA
| | - Thomas A. Kunkel
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
| | - Lars C. Pedersen
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
| | - Katarzyna Bebenek
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
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2
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Zhao B, Watanabe G, Lieber MR. Polymerase μ in non-homologous DNA end joining: importance of the order of arrival at a double-strand break in a purified system. Nucleic Acids Res 2020; 48:3605-3618. [PMID: 32052035 PMCID: PMC7144918 DOI: 10.1093/nar/gkaa094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/14/2020] [Accepted: 02/04/2020] [Indexed: 01/07/2023] Open
Abstract
During non-homologous DNA end joining (NHEJ), bringing two broken dsDNA ends into proximity is an essential prerequisite for ligation by XRCC4:Ligase IV (X4L4). This physical juxtaposition of DNA ends is called NHEJ synapsis. In addition to the key NHEJ synapsis proteins, Ku, X4L4, and XLF, it has been suggested that DNA polymerase mu (pol μ) may also align two dsDNA ends into close proximity for synthesis. Here, we directly observe the NHEJ synapsis by pol μ using a single molecule FRET (smFRET) assay where we can measure the duration of the synapsis. The results show that pol μ alone can mediate efficient NHEJ synapsis of 3′ overhangs that have at least 1 nt microhomology. The abundant Ku protein in cells limits the accessibility of pol μ to DNA ends with overhangs. But X4L4 can largely reverse the Ku inhibition, perhaps by pushing the Ku inward to expose the overhang for NHEJ synapsis. Based on these studies, the mechanistic flexibility known to exist at other steps of NHEJ is now also apparent for the NHEJ synapsis step.
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Affiliation(s)
- Bailin Zhao
- Department of Pathology, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology & Immunology, and Section of Computational & Molecular Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Ave, Rm. 5428, Los Angeles, CA 90089, USA
| | - Go Watanabe
- Department of Pathology, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology & Immunology, and Section of Computational & Molecular Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Ave, Rm. 5428, Los Angeles, CA 90089, USA
| | - Michael R Lieber
- Department of Pathology, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology & Immunology, and Section of Computational & Molecular Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Ave, Rm. 5428, Los Angeles, CA 90089, USA
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3
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Pol μ ribonucleotide insertion opposite 8-oxodG facilitates the ligation of premutagenic DNA repair intermediate. Sci Rep 2020; 10:940. [PMID: 31969622 PMCID: PMC6976671 DOI: 10.1038/s41598-020-57886-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/07/2020] [Indexed: 01/05/2023] Open
Abstract
DNA polymerase (pol) μ primarily inserts ribonucleotides into a single-nucleotide gapped DNA intermediate, and the ligation step plays a critical role in the joining of noncomplementary DNA ends during nonhomologous end joining (NHEJ) for the repair of double-strand breaks (DSBs) caused by reactive oxygen species. Here, we report that the pol μ insertion products of ribonucleotides (rATP or rCTP), instead of deoxyribonucleotides, opposite 8-oxo-2′-deoxyguanosine (8-oxodG) are efficiently ligated and the presence of Mn2+ stimulates this coupled reaction in vitro. Moreover, our results point to a role of pol μ in mediating ligation during the mutagenic bypass of 8-oxodG, while 3′-preinserted noncanonical base pairs (3′-rA or 3′-rC) on NHEJ repair intermediates compromise the end joining by DNA ligase I or the DNA ligase IV/XRCC4 complex.
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4
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Feng B, Wang K, Yang Y, Wang G, Zhang H, Liu Y, Jiang K. Ultrasensitive recognition of AP sites in DNA at the single-cell level: one molecular rotor sequentially self-regulated to form multiple different stable conformations. Chem Sci 2019; 10:10373-10380. [PMID: 32110326 PMCID: PMC6988597 DOI: 10.1039/c9sc04140k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/20/2019] [Indexed: 01/22/2023] Open
Abstract
Molecular rotors self-regulate their conformations to emit different ultrasensitive recognition signals for AP sites in DNA at the single-cell level.
The AP site is a primary form of DNA damage. Its presence alters the genetic structure and eventually causes malignant diseases. AP sites generally present a high-speed dynamic change in the DNA sequence. Thus, precisely recognizing AP sites is difficult, especially at the single-cell level. To address this issue, we provide a broad-spectrum strategy to design a group of molecular rotors, that is, a series of nonfluorescent 2-(4-vinylbenzylidene)malononitrile derivatives (BMN-Fluors), which constantly display molecular rotation in a free state. Interestingly, after activating the relevant specific-recognition reaction (i.e., hydrolysis reaction of benzylidenemalononitrile) only in the AP-site cavity within a short time (approximately 300 s), each of these molecules can be fixed into this cavity and can sequentially self-regulate to form different stable conformations in accordance with the cavity size. The different stable conformations possess various HOMO–LUMO energy gaps in their excited state. This condition enables the AP site to emit different fluorescence signals at various wavelengths. Given the different self-regulation abilities of the conformations, the series of molecules, BMN-Fluors, can emit different types of signals, including an “OFF–ON” single-channel signal, a “ratio” double-channel signal, and even a precise multichannel signal. Among the BMN-Fluors derivatives, d1-BMN can sequentially self-regulate to form five stable conformations, thereby resulting in the emission of a five-channel signal for different AP sites in situ. Thus, d1-BMN can be used as a probe to ultrasensitively recognize the AP site with precise fluorescent signals at the single-cell level. This design strategy can be generalized to develop additional single-channel to multichannel signal probes to recognize other specific sites in DNA sequences in living organisms.
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Affiliation(s)
- Beidou Feng
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Kui Wang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Yonggang Yang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Ge Wang
- Xinxiang Medical University , Xinxiang 453000 , P. R. China
| | - Hua Zhang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Yufang Liu
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Kai Jiang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
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5
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Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M. Structural evidence for an in trans base selection mechanism involving Loop1 in polymerase μ at an NHEJ double-strand break junction. J Biol Chem 2019; 294:10579-10595. [PMID: 31138645 DOI: 10.1074/jbc.ra119.008739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic DNA polymerase (Pol) X family members such as Pol μ and terminal deoxynucleotidyl transferase (TdT) are important components for the nonhomologous DNA end-joining (NHEJ) pathway. TdT participates in a specialized version of NHEJ, V(D)J recombination. It has primarily nontemplated polymerase activity but can take instructions across strands from the downstream dsDNA, and both activities are highly dependent on a structural element called Loop1. However, it is unclear whether Pol μ follows the same mechanism, because the structure of its Loop1 is disordered in available structures. Here, we used a chimeric TdT harboring Loop1 of Pol μ that recapitulated the functional properties of Pol μ in ligation experiments. We solved three crystal structures of this TdT chimera bound to several DNA substrates at 1.96-2.55 Å resolutions, including a full DNA double-strand break (DSB) synapsis. We then modeled the full Pol μ sequence in the context of one these complexes. The atomic structure of an NHEJ junction with a Pol X construct that mimics Pol μ in a reconstituted system explained the distinctive properties of Pol μ compared with TdT. The structure suggested a mechanism of base selection relying on Loop1 and taking instructions via the in trans templating base independently of the primer strand. We conclude that our atomic-level structural observations represent a paradigm shift for the mechanism of base selection in the Pol X family of DNA polymerases.
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Affiliation(s)
- Jérôme Loc'h
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
| | - Christina A Gerodimos
- the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology and the Department of Biological Sciences, Section of Molecular and Computational Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Sandrine Rosario
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
| | - Mustafa Tekpinar
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
| | - Michael R Lieber
- the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology and the Department of Biological Sciences, Section of Molecular and Computational Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Marc Delarue
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
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6
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Affiliation(s)
- Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258; Inserm UMR1068, Aix Marseille Université U105; Institut Paoli Calmettes, 27 Boulevard Lei Roure CS30059, 13273 Marseille, Cedex 09, France
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7
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Zou X, Owusu M, Harris R, Jackson SP, Loizou JI, Nik-Zainal S. Validating the concept of mutational signatures with isogenic cell models. Nat Commun 2018; 9:1744. [PMID: 29717121 PMCID: PMC5931590 DOI: 10.1038/s41467-018-04052-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/29/2018] [Indexed: 12/23/2022] Open
Abstract
The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy. Correlations between mutational signatures and environmental exposures, enzymatic activities and genetic defects have been described, but human cancers are not ideal experimental systems-the exposures to different mutational processes in a patient's lifetime are uncontrolled and any relationships observed can only be described as an association. Here, we demonstrate the proof-of-principle that it is possible to recreate cancer mutational signatures in vitro using CRISPR-Cas9-based gene-editing experiments in an isogenic human-cell system. We provide experimental and algorithmic methods to discover mutational signatures generated under highly experimentally-controlled conditions. Our in vitro findings strikingly recapitulate in vivo observations of cancer data, fundamentally validating the concept of (particularly) endogenously-arising mutational signatures.
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Affiliation(s)
- Xueqing Zou
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Michel Owusu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Rebecca Harris
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Stephen P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria.
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK.
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8
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Loc'h J, Delarue M. Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands. Curr Opin Struct Biol 2018; 53:22-31. [PMID: 29656238 DOI: 10.1016/j.sbi.2018.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 01/08/2023]
Abstract
Terminal deoxynucleotidyltransferase (TdT) is a member of the polX family which is involved in DNA repair. It has been known for years as an untemplated DNA polymerase used during V(D)J recombination to generate diversity at the CDR3 region of immunoglobulins and T-cell receptors. Recently, however, TdT was crystallized in the presence of a complete DNA synapsis made of two double-stranded DNA (dsDNA), each with a 3' protruding end, and overlapping with only one micro-homology base-pair, thus giving structural insight for the first time into DNA synthesis across strands. It was subsequently shown that TdT indeed has an in trans template-dependent activity in the presence of an excess of the downstream DNA duplex. A possible biological role of this dual activity is discussed.
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Affiliation(s)
- Jérôme Loc'h
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
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9
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Loc'h J, Rosario S, Delarue M. Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination. Structure 2016; 24:1452-63. [PMID: 27499438 DOI: 10.1016/j.str.2016.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/13/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022]
Abstract
Eukaryotic DNA polymerase of the polX family, such as pol μ and terminal deoxynucleotidyl transferase (TdT), are key components of the non-homologous end-joining or V(D)J recombination machinery, respectively. The established role of TdT is to add random nucleotides during V(D)J recombination. Here we show that TdT also has a templated-polymerase activity, similar to pol μ, in the presence of higher concentrations of a downstream DNA duplex, and performs a micro-homology single base-pair search to align the DNA synapsis. To understand the molecular basis of this alignment, we solve crystal structures of TdT with four DNA strands and study the influence of the 3' protruding end. Two mutations in TdT inspired by sequence alignments with pol μ further improve the templated activity. We propose that both templated and untemplated activities of TdT are needed to explain the distributions of lengths of N regions observed experimentally in T cell receptors and antibodies.
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Affiliation(s)
- Jérôme Loc'h
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., 25 rue du Dr Roux, 75015 Paris, France
| | - Sandrine Rosario
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., 25 rue du Dr Roux, 75015 Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., 25 rue du Dr Roux, 75015 Paris, France.
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10
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Molecular Dynamics Simulations and Structural Analysis to Decipher Functional Impact of a Twenty Residue Insert in the Ternary Complex of Mus musculus TdT Isoform. PLoS One 2016; 11:e0157286. [PMID: 27311013 PMCID: PMC4911049 DOI: 10.1371/journal.pone.0157286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 05/26/2016] [Indexed: 01/08/2023] Open
Abstract
Insertions/deletions are common evolutionary tools employed to alter the structural and functional repertoire of protein domains. An insert situated proximal to the active site or ligand binding site frequently impacts protein function; however, the effect of distal indels on protein activity and/or stability are often not studied. In this paper, we have investigated a distal insert, which influences the function and stability of a unique DNA polymerase, called terminal deoxynucleotidyl transferase (TdT). TdT (EC:2.7.7.31) is a monomeric 58 kDa protein belonging to family X of eukaryotic DNA polymerases and known for its role in V(D)J recombination as well as in non-homologous end-joining (NHEJ) pathways. Two murine isoforms of TdT, with a length difference of twenty residues and having different biochemical properties, have been studied. All-atom molecular dynamics simulations at different temperatures and interaction network analyses were performed on the short and long-length isoforms. We observed conformational changes in the regions distal to the insert position (thumb subdomain) in the longer isoform, which indirectly affects the activity and stability of the enzyme through a mediating loop (Loop1). A structural rationale could be provided to explain the reduced polymerization rate as well as increased thermosensitivity of the longer isoform caused by peripherally located length variations within a DNA polymerase. These observations increase our understanding of the roles of length variants in introducing functional diversity in protein families in general.
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11
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Essential role for polymerase specialization in cellular nonhomologous end joining. Proc Natl Acad Sci U S A 2015; 112:E4537-45. [PMID: 26240371 DOI: 10.1073/pnas.1505805112] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nonhomologous end joining (NHEJ) repairs chromosome breaks and must remain effective in the face of extensive diversity in broken end structures. We show here that this flexibility is often reliant on the ability to direct DNA synthesis across strand breaks, and that polymerase (Pol) μ and Pol λ are the only mammalian DNA polymerases that have this activity. By systematically varying substrate in cells, we show each polymerase is uniquely proficient in different contexts. The templating nucleotide is also selected differently, with Pol μ using the unpaired base adjacent to the downstream 5' phosphate even when there are available template sites further upstream of this position; this makes Pol μ more flexible but also less accurate than Pol λ. Loss of either polymerase alone consequently has clear and distinguishable effects on the fidelity of repair, but end remodeling by cellular nucleases and the remaining polymerase helps mitigate the effects on overall repair efficiency. Accordingly, when cells are deficient in both polymerases there is synergistic impact on NHEJ efficiency, both in terms of repair of defined substrates and cellular resistance to ionizing radiation. Pol μ and Pol λ thus provide distinct solutions to a problem for DNA synthesis that is unique to this pathway and play a key role in conferring on NHEJ the flexibility required for accurate and efficient repair.
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12
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Gouge J, Rosario S, Romain F, Poitevin F, Béguin P, Delarue M. Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair. EMBO J 2015; 34:1126-42. [PMID: 25762590 PMCID: PMC4406656 DOI: 10.15252/embj.201489643] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 01/18/2023] Open
Abstract
Eukaryotic DNA polymerase mu of the PolX family can promote the association of the two 3'-protruding ends of a DNA double-strand break (DSB) being repaired (DNA synapsis) even in the absence of the core non-homologous end-joining (NHEJ) machinery. Here, we show that terminal deoxynucleotidyltransferase (TdT), a closely related PolX involved in V(D)J recombination, has the same property. We solved its crystal structure with an annealed DNA synapsis containing one micro-homology (MH) base pair and one nascent base pair. This structure reveals how the N-terminal domain and Loop 1 of Tdt cooperate for bridging the two DNA ends, providing a templating base in trans and limiting the MH search region to only two base pairs. A network of ordered water molecules is proposed to assist the incorporation of any nucleotide independently of the in trans templating base. These data are consistent with a recent model that explains the statistics of sequences synthesized in vivo by Tdt based solely on this dinucleotide step. Site-directed mutagenesis and functional tests suggest that this structural model is also valid for Pol mu during NHEJ.
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Affiliation(s)
- Jérôme Gouge
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., Paris, France
| | - Sandrine Rosario
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., Paris, France
| | - Félix Romain
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., Paris, France
| | - Frédéric Poitevin
- Institut de Physique Théorique, CEA-Saclay, CNRS URA 2306, Gif-sur-Yvette, France
| | - Pierre Béguin
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., Paris, France
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