Structural Basis of DNA Synthesis Opposite 8-oxoguanine by Human PrimPol Primase-polymerase

Overview

Journal Nat Commun

Specialty Biology

Date 2021 Jun 30

PMID 34188055

Citations 12

Authors

Olga Rechkoblit

Robert E Johnson

Yogesh K Gupta

Louise Prakash

Satya Prakash

Aneel K Aggarwal

Affiliations

Soon will be listed here.

Abstract

PrimPol is a human DNA polymerase-primase that localizes to mitochondria and nucleus and bypasses the major oxidative lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis, in mostly error-free manner. We present structures of PrimPol insertion complexes with a DNA template-primer and correct dCTP or erroneous dATP opposite the lesion, as well as extension complexes with C or A as a 3'-terminal primer base. We show that during the insertion of C and extension from it, the active site is unperturbed, reflecting the readiness of PrimPol to accommodate oxoG(anti). The misinsertion of A opposite oxoG(syn) also does not alter the active site, and is likely less favorable due to lower thermodynamic stability of the oxoG(syn)•A base-pair. During the extension step, oxoG(syn) induces an opening of its base-pair with A or misalignment of the 3'-A primer terminus. Together, the structures show how PrimPol accurately synthesizes DNA opposite oxidatively damaged DNA in human cells.

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References

Hsu G, Ober M, Carell T, Beese L . Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature. 2004; 431(7005):217-21. DOI: 10.1038/nature02908. View

Batra V, Shock D, Beard W, McKenna C, Wilson S . Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion. Proc Natl Acad Sci U S A. 2011; 109(1):113-8. PMC: 3252918. DOI: 10.1073/pnas.1112235108. View

Markkanen E, Castrec B, Villani G, Hubscher U . A switch between DNA polymerases δ and λ promotes error-free bypass of 8-oxo-G lesions. Proc Natl Acad Sci U S A. 2012; 109(50):20401-6. PMC: 3528542. DOI: 10.1073/pnas.1211532109. View

Bailey L, Bianchi J, Doherty A . PrimPol is required for the maintenance of efficient nuclear and mitochondrial DNA replication in human cells. Nucleic Acids Res. 2019; 47(8):4026-4038. PMC: 6486543. DOI: 10.1093/nar/gkz056. View

Tubbs A, Nussenzweig A . Endogenous DNA Damage as a Source of Genomic Instability in Cancer. Cell. 2017; 168(4):644-656. PMC: 6591730. DOI: 10.1016/j.cell.2017.01.002. View

Zorov D, Juhaszova M, Sollott S . Mitochondrial reactive oxygen species (ROS) and ROS-induced ROS release. Physiol Rev. 2014; 94(3):909-50. PMC: 4101632. DOI: 10.1152/physrev.00026.2013. View

Cadet J, Douki T, Gasparutto D, Ravanat J . Oxidative damage to DNA: formation, measurement and biochemical features. Mutat Res. 2003; 531(1-2):5-23. DOI: 10.1016/j.mrfmmm.2003.09.001. View

Kauppila J, Bonekamp N, Mourier A, Isokallio M, Just A, Kauppila T . Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice. Nucleic Acids Res. 2018; 46(13):6642-6669. PMC: 6061787. DOI: 10.1093/nar/gky456. View

Krasich R, Copeland W . DNA polymerases in the mitochondria: A critical review of the evidence. Front Biosci (Landmark Ed). 2016; 22(4):692-709. PMC: 5485829. DOI: 10.2741/4510. View

10.

Shibutani S, Takeshita M, Grollman A . Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature. 1991; 349(6308):431-4. DOI: 10.1038/349431a0. View

11.

Burak M, Guja K, Hambardjieva E, Derkunt B, Garcia-Diaz M . A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. EMBO J. 2016; 35(18):2045-59. PMC: 5282837. DOI: 10.15252/embj.201694332. View

12.

Mouret S, Forestier A, Douki T . The specificity of UVA-induced DNA damage in human melanocytes. Photochem Photobiol Sci. 2011; 11(1):155-62. DOI: 10.1039/c1pp05185g. View

13.

Brieba L, Eichman B, Kokoska R, Doublie S, Kunkel T, Ellenberger T . Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. EMBO J. 2004; 23(17):3452-61. PMC: 516626. DOI: 10.1038/sj.emboj.7600354. View

14.

Quiros P, Mottis A, Auwerx J . Mitonuclear communication in homeostasis and stress. Nat Rev Mol Cell Biol. 2016; 17(4):213-26. DOI: 10.1038/nrm.2016.23. View

15.

Gao Y, Yang W . Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis. Science. 2016; 352(6291):1334-7. PMC: 6320252. DOI: 10.1126/science.aad9633. View

16.

Haracska L, Yu S, Johnson R, Prakash L, Prakash S . Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta. Nat Genet. 2000; 25(4):458-61. DOI: 10.1038/78169. View

17.

Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov N . Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. PLoS Biol. 2005; 4(1):e11. PMC: 1325099. DOI: 10.1371/journal.pbio.0040011. View

18.

Neeley W, Essigmann J . Mechanisms of formation, genotoxicity, and mutation of guanine oxidation products. Chem Res Toxicol. 2006; 19(4):491-505. DOI: 10.1021/tx0600043. View

19.

Keen B, Jozwiakowski S, Bailey L, Bianchi J, Doherty A . Molecular dissection of the domain architecture and catalytic activities of human PrimPol. Nucleic Acids Res. 2014; 42(9):5830-45. PMC: 4027207. DOI: 10.1093/nar/gku214. View

20.

Nakamura T, Zhao Y, Yamagata Y, Hua Y, Yang W . Watching DNA polymerase η make a phosphodiester bond. Nature. 2012; 487(7406):196-201. PMC: 3397672. DOI: 10.1038/nature11181. View