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Plugged Into the Ku-DNA Hub: the NHEJ Network Philippe Frit, Virginie Ropars, Mauro Modesti, Jean-Baptiste Charbonnier, Patrick Calsou

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Plugged Into the Ku-DNA Hub: the NHEJ Network Philippe Frit, Virginie Ropars, Mauro Modesti, Jean-Baptiste Charbonnier, Patrick Calsou Plugged into the Ku-DNA hub: The NHEJ network Philippe Frit, Virginie Ropars, Mauro Modesti, Jean-Baptiste Charbonnier, Patrick Calsou To cite this version: Philippe Frit, Virginie Ropars, Mauro Modesti, Jean-Baptiste Charbonnier, Patrick Calsou. Plugged into the Ku-DNA hub: The NHEJ network. Progress in Biophysics and Molecular Biology, Elsevier, 2019, 147, pp.62-76. 10.1016/j.pbiomolbio.2019.03.001. hal-02144114 HAL Id: hal-02144114 https://hal.archives-ouvertes.fr/hal-02144114 Submitted on 29 May 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Progress in Biophysics and Molecular Biology xxx (xxxx) xxx Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio Plugged into the Ku-DNA hub: The NHEJ network * Philippe Frit a, b, Virginie Ropars c, Mauro Modesti d, e, Jean Baptiste Charbonnier c, , ** Patrick Calsou a, b, a Institut de Pharmacologie et Biologie Structurale, IPBS, Universite de Toulouse, CNRS, UPS, Toulouse, France b Equipe Labellisee Ligue Contre le Cancer, Toulouse, France c Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ. Paris-Sud, Universite Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France d Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Universite UM105, Marseille, France e Equipe Labellisee Ligue Contre le Cancer, Marseille, France article info abstract Article history: In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining Received 31 October 2018 (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a Received in revised form recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the 26 February 2019 Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To Accepted 1 March 2019 shed light on these dynamic interplays, we review here current knowledge on proteins directly inter- Available online xxx acting with Ku and on the contact points involved, with a particular accent on the different classes of Ku- binding motifs identified in several Ku partners. An integrated structural model of the core NHEJ network Keywords: DNA damage at the synapsis step is proposed. © NHEJ 2019 Elsevier Ltd. All rights reserved. Double-strand breaks Ku Protein interactions network DNA repair machineries Conserved binding motifs Contents 1. Introduction . ................................................. 00 2. The Ku-DNA hub . ................................................. 00 3. DNA-PKcs ................................................................. ....... ................................................. 00 4. Proteins containing a unique Ku-binding Motif (KBM) . .................................... 00 4.1. APLF................................................................ ................................ ....................... 00 4.2. XLF/Cernunnos . ....................... 00 4.3. PAXX ................................................................................................ ....................... 00 4.4. The X-family DNA polymerases . ....................... 00 5. Proteins containing several KBMs . ............................................ 00 5.1. CYREN/MRI .......................................................................................... ....................... 00 Abbreviations: APLF, APTX and PNKP-like factor; BRCT, BRCA1 C-Terminus domain; Cryo-EM, cryo-electron microscopy; CTD, C-terminal domain; CYREN, cell-cycle regulator of NHEJ; DNA-PK, DNA-dependent protein kinase; DNA-PKcs, DNA-PK catalytic subunit; ds, double-stranded; DSB, DNA double strand break; EMSA, electrophoretic mobility shift assay; HEAT, Huntington, Elongation Factor 3; PR65/A, TOR domain; FAT, FRAP, ATM and TRRAP domain; FATC, FAT and C-terminal domain; FHA, forkhead associated domain; IR, ionizing radiation; KBM, Ku-binding motif; KD, kinase domain; MRI, modulator of retroviral infection; NAP1L, nucleosome assembly protein 1-like domain; PAXX, paralog of XRCC4 and XLF; PBZ, PAR Binding Zinc finger domain; PI3K, phosphatidyl inositol 3 kinase; PIKK, phosphatidyl inositol-3 kinase-like protein kinase; PNKP, Polynucleotide Kinase/Phosphatase; RAG1, Recombination activating gene 1; TDP1, Tyrosyl-DNA phosphodiesterase 1; TdT, terminal deoxynucleotidyl transferase; Top1, Top2, DNA topoisomerase 1, 2; vWA, von Willebrand factor type A; XLF, XRCC4-Like Factor; WS, Werner Syndrome. * Corresponding author. Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ. Paris-Sud, Universite Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France. ** Corresponding author. Institut de Pharmacologie et Biologie Structurale, IPBS, Universite de Toulouse, CNRS, UPS, Toulouse, France. E-mail addresses: [email protected] (J.B. Charbonnier), [email protected] (P. Calsou). https://doi.org/10.1016/j.pbiomolbio.2019.03.001 0079-6107/© 2019 Elsevier Ltd. All rights reserved. Please cite this article as: Frit, P et al., Plugged into the Ku-DNA hub: The NHEJ network, Progress in Biophysics and Molecular Biology, https:// doi.org/10.1016/j.pbiomolbio.2019.03.001 2 P. Frit et al. / Progress in Biophysics and Molecular Biology xxx (xxxx) xxx 5.2. WRN ..................................................................... .................................................. 00 6. Comments on KBMs and KBM-binding sites on Ku . ..................... 00 7. Bring them all together! . ..................... 00 Acknowledgments . .................................................. 00 Supplementary data . ..................... 00 References . .................................................. 00 1. Introduction XRCC4 and XLF/Cernunnos), enzymatic activities involved in NHEJ fall into several classes that are more or less required depending on DNA double-strand breaks (DSBs) consist in the localized the DNA ends chemical complexity: protein kinase (DNA-depen- breakage of both DNA strands. DSBs are genomic lesions particu- dent protein kinase catalytic subunit - DNA-PKcs), nucleases (APLF, larly deleterious for cell homeostasis since when unrepaired or Artemis, Werner protein (WRN)), DNA helicase (WRN), tyrosyl- misrepaired, they can lead to cell death or to cancer-prone chro- DNA phosphodiesterase (TDP1), polynucleotide Kinase/Phospha- mosomal aberrations (Mladenov et al., 2016). DSBs can occur from tase (PNKP), DNA deadenylase (Aprataxin), DNA polymerases (Polm cell exposure to ionizing radiations or radiomimetic compounds, all and Poll) or terminal deoxynucleotidyl transferase (TdT) (Chang generating breaks with two DNA ends that are generally chemically et al., 2017)(Fig. 1). heterogeneous (Schipler and Iliakis, 2013). In vertebrates, DSBs Although several structures of components of the NHEJ ma- with two ends are also intermediates in physiological processes like chinery, alone or in a complex, have been determined (Ochi et al., V(D)J recombination in lymphocyte progenitors that rearrange 2014; Williams et al., 2014)(Fig. 1), a complete view of the dy- immunoglobulin and T-cell receptor genes (Alt et al., 2013)orDNA namic interactions between all these components is lacking. Here, breakage associated with neural development and the functioning we focus on the human Ku-DNA hub. We review current knowledge of mature neurons (Alt and Schwer, 2018). A subclass of DSBs on its direct interactants and on the contact points involved, with a bearing only one DNA end arises during DNA replication when the particular accent on the different classes of Ku-binding motifs replication fork encounters single-strand breaks, or by cutting of (KBMs) identified so far in several Ku protein partners (Fig. 2). stalled replication forks by structure-specific endonucleases Comparison with equivalent features or structures in yeast will be (Pasero and Vindigni, 2017). punctually emphasized. Finally, based on the available data, an In vertebrates, the majority of DSBs with two ends is repaired by integrated structural model of the core NHEJ network at the syn- Non-Homologous End-Joining (NHEJ) (Chang et al., 2017; Lieber, apsis step is proposed. 2010; Waters et al., 2014). Dysfunctions in core NHEJ factors translate into syndromes associating immunodeficiency, micro- cephaly and increased cell radiosensitivity (de Villartay, 2015; 2. The Ku-DNA hub Woodbine et al., 2014). End-joining of DSBs is also active in some bacterial species (Bertrand et al., 2019; Glickman, 2014), in yeasts The human Ku70 (70 kDa) and Ku80 (80 kDa) subunits present a (Emerson and Bertuch, 2016) and in ciliates (Marmignon et al., common topology and domain organization with an N-terminal a/b 2014). domain that belongs to the von Willebrand (vWA) family, a central DSB recognition involves the threading onto the extremities of domain (b-barrel, pillar, bridge), a C-terminal arm and a helical C- the DSB of the ring-shaped Ku heterodimer composed of subunits
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