Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair

Jamsen, Joonas A.; Sassa, Akira; Perera, Lalith; Shock, David D.; Beard, William A.; Wilson, Samuel H.

doi:10.1038/s41467-021-24486-x

Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair

Journal Article · Fri Aug 20 00:00:00 EDT 2021 · Nature Communications

DOI:https://doi.org/10.1038/s41467-021-24486-x· OSTI ID:1814983

^[1]; Sassa, Akira ^[2]; ^[1]; Shock, David D. ^[1]; Beard, William A. ^[1]; ^[1]

National Inst. of Health (NIH), Research Triangle Park, NC (United States). National Inst. of Environmental Health Sciences. Genome Integrity and Structural Biology Lab.
Chiba Univ. (Japan). Lab. of Chromatin Metabolism and Epigenetics. Graduate School of Science

Reactive oxygen species (ROS) oxidize cellular nucleotide pools and cause double strand breaks (DSBs). Non-homologous end-joining (NHEJ) attaches broken chromosomal ends together in mammalian cells. Ribonucleotide insertion by DNA polymerase (pol) μ prepares breaks for end-joining and this is required for successful NHEJ in vivo. We previously showed that pol μ lacks discrimination against oxidized dGTP (8-oxo-dGTP), that can lead to mutagenesis, cancer, aging and human disease. Here we reveal the structural basis for proficient oxidized ribonucleotide (8-oxo-rGTP) incorporation during DSB repair by pol μ. Time-lapse crystallography snapshots of structural intermediates during nucleotide insertion along with computational simulations reveal substrate, metal and side chain dynamics, that allow oxidized ribonucleotides to escape polymerase discrimination checkpoints. Abundant nucleotide pools, combined with inefficient sanitization and repair, implicate pol μ mediated oxidized ribonucleotide insertion as an emerging source of widespread persistent mutagenesis and genomic instability.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI ID:: 1814983

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 12; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (53)

Crystallographic evidence for two‐metal‐ion catalysis in human pol η Wang, Jimin; Smithline, Zachary B. Protein Science, Vol. 28, Issue 2 https://doi.org/10.1002/pro.3541	journal	December 2018
Physiological concentrations of purines and pyrimidines Traut, Thomas W. Molecular and Cellular Biochemistry, Vol. 140, Issue 1 https://doi.org/10.1007/BF00928361	journal	January 1994
Functional cooperation of MutT, MutM and MutY proteins in preventing mutations caused by spontaneous oxidation of guanine nucleotide in Escherichia coli Tajiri, Tatsurou; Maki, Hisaji; Sekiguchi, Mutsuo Mutation Research/DNA Repair, Vol. 336, Issue 3 https://doi.org/10.1016/0921-8777(94)00062-B	journal	May 1995
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Oxygen Metabolism Causes Chromosome Breaks and Is Associated with the Neuronal Apoptosis Observed in DNA Double-Strand Break Repair Mutants Karanjawala, Zarir E.; Murphy, Niamh; Hinton, David R. Current Biology, Vol. 12, Issue 5 https://doi.org/10.1016/S0960-9822(02)00684-X	journal	March 2002
Repair of oxidatively damaged guanine in Saccharomyces cerevisiae by an alternative pathway Bruner, Steven D.; Nash, Huw M.; Lane, William S. Current Biology, Vol. 8, Issue 7 https://doi.org/10.1016/S0960-9822(98)70158-7	journal	March 1998
Observing a DNA Polymerase Choose Right from Wrong Freudenthal, Bret D.; Beard, William A.; Shock, David D. Cell, Vol. 154, Issue 1 https://doi.org/10.1016/j.cell.2013.05.048	journal	July 2013
Assessing biomarkers of oxidative stress: Analysis of guanosine and oxidized guanosine nucleotide triphosphates by high performance liquid chromatography with electrochemical detection Bolin, Celeste; Cardozo-Pelaez, Fernando Journal of Chromatography B, Vol. 856, Issue 1-2 https://doi.org/10.1016/j.jchromb.2007.05.034	journal	September 2007
RNase H2-Initiated Ribonucleotide Excision Repair Sparks, Justin L.; Chon, Hyongi; Cerritelli, Susana M. Molecular Cell, Vol. 47, Issue 6 https://doi.org/10.1016/j.molcel.2012.06.035	journal	September 2012
DNA polymerases involved in the incorporation of oxidized nucleotides into DNA: Their efficiency and template base preference Katafuchi, Atsushi; Nohmi, Takehiko Mutation Research/Genetic Toxicology and Environmental Mutagenesis, Vol. 703, Issue 1 https://doi.org/10.1016/j.mrgentox.2010.06.004	journal	November 2010
Metabolic Fate of Oxidized Guanine Ribonucleotides in Mammalian Cells ^† Hayakawa, Hiroshi; Hofer, Anders; Thelander, Lars Biochemistry, Vol. 38, Issue 12 https://doi.org/10.1021/bi982361l	journal	March 1999
Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment Fonseca Guerra, Célia; Bickelhaupt, F. Matthias; Snijders, Jaap G. Journal of the American Chemical Society, Vol. 122, Issue 17 https://doi.org/10.1021/ja993262d	journal	May 2000
Instability and decay of the primary structure of DNA Lindahl, Tomas Nature, Vol. 362, Issue 6422 https://doi.org/10.1038/362709a0	journal	April 1993
Watching DNA polymerase η make a phosphodiester bond Nakamura, Teruya; Zhao, Ye; Yamagata, Yuriko Nature, Vol. 487, Issue 7406 https://doi.org/10.1038/nature11181	journal	July 2012
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide Freudenthal, Bret D.; Beard, William A.; Perera, Lalith Nature, Vol. 517, Issue 7536 https://doi.org/10.1038/nature13886	journal	November 2014
Genome instability due to ribonucleotide incorporation into DNA McElhinny, Stephanie A. Nick; Kumar, Dinesh; Clark, Alan B. Nature Chemical Biology, Vol. 6, Issue 10 https://doi.org/10.1038/nchembio.424	journal	August 2010
Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ Swan, Michael K.; Johnson, Robert E.; Prakash, Louise Nature Structural & Molecular Biology, Vol. 16, Issue 9 https://doi.org/10.1038/nsmb.1663	journal	August 2009
Sustained active site rigidity during synthesis by human DNA polymerase μ Moon, Andrea F.; Pryor, John M.; Ramsden, Dale A. Nature Structural & Molecular Biology, Vol. 21, Issue 3 https://doi.org/10.1038/nsmb.2766	journal	February 2014
Time-lapse crystallography snapshots of a double-strand break repair polymerase in action Jamsen, Joonas A.; Beard, William A.; Pedersen, Lars C. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00271-7	journal	August 2017
Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide Jamsen, Joonas A.; Sassa, Akira; Shock, David D. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21354-6	journal	April 2021
Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse Perera, Lalith; Freudenthal, Bret D.; Beard, William A. Proceedings of the National Academy of Sciences, Vol. 112, Issue 38 https://doi.org/10.1073/pnas.1511207112	journal	September 2015
Oxidants, antioxidants, and the degenerative diseases of aging. Ames, B. N.; Shigenaga, M. K.; Hagen, T. M. Proceedings of the National Academy of Sciences, Vol. 90, Issue 17 https://doi.org/10.1073/pnas.90.17.7915	journal	September 1993
A Molecular Basis for the Selective Recognition of 2-Hydroxy-dATP and 8-Oxo-dGTP by Human MTH1 Sakai, Yasunari; Furuichi, Masato; Takahashi, Masayuki Journal of Biological Chemistry, Vol. 277, Issue 10 https://doi.org/10.1074/jbc.M110566200	journal	March 2002
Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion Cavanaugh, Nisha A.; Beard, William A.; Batra, Vinod K. Journal of Biological Chemistry, Vol. 286, Issue 36 https://doi.org/10.1074/jbc.M111.253401	journal	July 2011
Elimination and Utilization of Oxidized Guanine Nucleotides in the Synthesis of RNA and Its Precursors Sekiguchi, Takeshi; Ito, Riyoko; Hayakawa, Hiroshi Journal of Biological Chemistry, Vol. 288, Issue 12 https://doi.org/10.1074/jbc.M112.418723	journal	March 2013
Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences Cilli, Piera; Minoprio, Anna; Bossa, Cecilia Journal of Biological Chemistry, Vol. 290, Issue 43 https://doi.org/10.1074/jbc.M115.679209	journal	October 2015
Impact of Ribonucleotide Backbone on Translesion Synthesis and Repair of 7,8-Dihydro-8-oxoguanine Sassa, Akira; Çağlayan, Melike; Rodriguez, Yesenia Journal of Biological Chemistry, Vol. 291, Issue 46 https://doi.org/10.1074/jbc.M116.738732	journal	November 2016
DNA polymerase mu (Pol micro), homologous to TdT, could act as a DNA mutator in eukaryotic cells Dominguez, O. The EMBO Journal, Vol. 19, Issue 7 https://doi.org/10.1093/emboj/19.7.1731	journal	April 2000
Hydroxylation of deoxyguanosine at the C-8 position by ascorbic acid and other reducing agents Kasai, Hiroshi; Nishimura, Susumu Nucleic Acids Research, Vol. 12, Issue 4 https://doi.org/10.1093/nar/12.4.2137	journal	January 1984
Lack of sugar discrimination by human Pol requires a single glycine residue Ruiz, J. F. Nucleic Acids Research, Vol. 31, Issue 15 https://doi.org/10.1093/nar/gkg637	journal	August 2003
Trace amounts of 8-oxo-dGTP in mitochondrial dNTP pools reduce DNA polymerase replication fidelity Pursell, Z. F.; McDonald, J. T.; Mathews, C. K. Nucleic Acids Research, Vol. 36, Issue 7 https://doi.org/10.1093/nar/gkn062	journal	February 2008
Quantitation of cellular deoxynucleoside triphosphates Ferraro, Paola; Franzolin, Elisa; Pontarin, Giovanna Nucleic Acids Research, Vol. 38, Issue 6 https://doi.org/10.1093/nar/gkp1141	journal	December 2009
Ribonucleotides and manganese ions improve non-homologous end joining by human Polµ Martin, Maria Jose; Garcia-Ortiz, Maria V.; Esteban, Veronica Nucleic Acids Research, Vol. 41, Issue 4 https://doi.org/10.1093/nar/gks1444	journal	December 2012
The catalytic cycle for ribonucleotide incorporation by human DNA Pol λ Gosavi, Rajendrakumar A.; Moon, Andrea F.; Kunkel, Thomas A. Nucleic Acids Research, Vol. 40, Issue 15 https://doi.org/10.1093/nar/gks413	journal	May 2012
Mycobacterium smegmatis DinB2 misincorporates deoxyribonucleotides and ribonucleotides during templated synthesis and lesion bypass Ordonez, Heather; Shuman, Stewart Nucleic Acids Research, Vol. 42, Issue 20 https://doi.org/10.1093/nar/gku1027	journal	October 2014
ATP insertion opposite 8-oxo-deoxyguanosine by Pol4 mediates error-free tolerance in Schizosaccharomyces pombe Sastre-Moreno, Guillermo; Sánchez, Arancha; Esteban, Verónica Nucleic Acids Research, Vol. 42, Issue 15 https://doi.org/10.1093/nar/gku711	journal	August 2014
Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu Moon, Andrea F.; Pryor, John M.; Ramsden, Dale A. Nucleic Acids Research, Vol. 45, Issue 15 https://doi.org/10.1093/nar/gkx527	journal	June 2017
Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2 Malfatti, Matilde Clarissa; Balachander, Sathya; Antoniali, Giulia Nucleic Acids Research, Vol. 45, Issue 19 https://doi.org/10.1093/nar/gkx723	journal	August 2017
Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2′-guanosine Kaminski, Andrea M.; Chiruvella, Kishore K.; Ramsden, Dale A. Nucleic Acids Research, Vol. 47, Issue 17 https://doi.org/10.1093/nar/gkz680	journal	August 2019
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906019949	journal	July 2006
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Oxidation of the Guanine Nucleotide Pool Underlies Cell Death by Bactericidal Antibiotics Foti, J. J.; Devadoss, B.; Winkler, J. A. Science, Vol. 336, Issue 6079 https://doi.org/10.1126/science.1219192	journal	April 2012
Counteraction by MutT Protein of Transcriptional Errors Caused by Oxidative Damage Taddei, F.; Hayakawa, H.; Bouton, M. -F. Science, Vol. 278, Issue 5335 https://doi.org/10.1126/science.278.5335.128	journal	October 1997
Impairment of V(D)J recombination in double-strand break repair mutants Taccioli, G.; Rathbun, G.; Oltz, E. Science, Vol. 260, Issue 5105 https://doi.org/10.1126/science.8469973	journal	April 1993
Capture of a third Mg2+ is essential for catalyzing DNA synthesis Gao, Y.; Yang, W. Science, Vol. 352, Issue 6291 https://doi.org/10.1126/science.aad9633	journal	June 2016
Ribonucleotide incorporation enables repair of chromosome breaks by nonhomologous end joining Pryor, John M.; Conlin, Michael P.; Carvajal-Garcia, Juan Science, Vol. 361, Issue 6407 https://doi.org/10.1126/science.aat2477	journal	September 2018
Polymerase Mu Is a DNA-Directed DNA/RNA Polymerase Nick McElhinny, S. A.; Ramsden, D. A. Molecular and Cellular Biology, Vol. 23, Issue 7 https://doi.org/10.1128/MCB.23.7.2309-2315.2003	journal	April 2003
Modernizing the Nonhomologous End-Joining Repertoire: Alternative and Classical NHEJ Share the Stage Deriano, Ludovic; Roth, David B. Annual Review of Genetics, Vol. 47, Issue 1 https://doi.org/10.1146/annurev-genet-110711-155540	journal	November 2013
Mutations induced by 8-hydroxyguanine (8-oxo-7,8-dihydroguanine), a representative oxidized base, in mammalian cells Suzuki, Tetsuya; Kamiya, Hiroyuki Genes and Environment, Vol. 39, Issue 1 https://doi.org/10.1186/s41021-016-0051-y	journal	December 2016
Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli Moore, Jessica M.; Correa, Raul; Rosenberg, Susan M. PLOS Genetics, Vol. 13, Issue 7 https://doi.org/10.1371/journal.pgen.1006733	journal	July 2017
Topoisomerase I‐mediated cleavage at unrepaired ribonucleotides generates DNA double‐strand breaks Huang, Shar‐yin N.; Williams, Jessica S.; Arana, Mercedes E. The EMBO Journal, Vol. 36, Issue 3 https://doi.org/10.15252/embj.201592426	journal	February 2017
RHINO forms a stoichiometric complex with the 9-1-1 checkpoint clamp and mediates ATR-Chk1 signaling Lindsey-Boltz, Laura A.; Kemp, Michael G.; Capp, Christopher Cell Cycle, Vol. 14, Issue 1 https://doi.org/10.4161/15384101.2014.967076	journal	January 2015

Similar Records

Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide

Journal Article · Mon Apr 05 20:00:00 EDT 2021 · Nature Communications · OSTI ID:1783881

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide

Journal Article · Sun Nov 16 19:00:00 EST 2014 · Nature (London) · OSTI ID:1168869

Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break

Journal Article · Mon Sep 21 20:00:00 EDT 2020 · Nature Communications · OSTI ID:1669125

Related Subjects

60 APPLIED LIFE SCIENCES
X-ray crystallography
cancer
enzyme mechanisms

Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair

Citation Formats

References (53)

Similar Records

Related Subjects