DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion

A major base lesion resulting from oxidative stress is 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxoG) that has ambiguous coding potential. Error-free DNA synthesis involves 8-oxoG adopting an anti-conformation to base pair with cytosine whereas mutagenic bypass involves 8-oxoG adopting a syn-conformation to base pair with adenine. Left unrepaired the syn-8-oxoG/dAMP base pair results in a G–C to T–A transversion. During base excision repair of this mispair, DNA polymerase (pol) β is confronted with gap filling opposite 8-oxoG. To determine how pol β discriminates between anti- and syn-8-oxoG, we introduced a point mutation (R283K) to alter insertion specificity. Kinetic studies demonstrate that this substitution results in an increased fidelity opposite 8-oxoG. Structural studies with R283K pol β show that the binary DNA complex has 8-oxoG in equilibrium between anti- and syn-forms. Ternary complexes with incoming dCTP resemble the wild-type enzyme, with templating anti-8-oxoG base pairing with incoming cytosine. In contrast to wild-type pol β, the ternary complex of the R283K mutant with an incoming dATP-analogue and templating 8-oxoG resembles a G–A mismatched structure with 8-oxoG adopting an anti-conformation. These results demonstrate that the incoming nucleotide is unable to induce a syn-8-oxoG conformation without minor groove DNA polymerase interactions that influence templating (anti-/syn-equilibrium) of 8-oxoG while modulating fidelity.

[1]  Samuel H. Wilson,et al.  [11] Purification and domain-mapping of mammalian DNA polymerase β , 1995 .

[2]  Samuel H. Wilson,et al.  Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. , 2003, Structure.

[3]  Samuel H. Wilson,et al.  Structures of dNTP intermediate states during DNA polymerase active site assembly. , 2012, Structure.

[4]  Samuel H. Wilson,et al.  DNA polymerase beta ribonucleotide discrimination: insertion, misinsertion, extension, and coding. , 2010, The Journal of biological chemistry.

[5]  A. Grollman,et al.  Mutagenesis by 8-oxoguanine: an enemy within. , 1993, Trends in genetics : TIG.

[6]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[7]  A. Grollman,et al.  Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG , 1991, Nature.

[8]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[9]  S. H. Wilson,et al.  8-oxodGTP incorporation by DNA polymerase beta is modified by active-site residue Asn279. , 2000, Biochemistry.

[10]  Samuel H. Wilson,et al.  DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". , 2009, The Journal of biological chemistry.

[11]  D. Patel,et al.  NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-Oxo-7H-dG(syn).dA(anti) alignment at lesion site. , 1991, Biochemistry.

[12]  M. Egli,et al.  Hydrogen Bonding of 7,8-Dihydro-8-oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus solfataricus DNA Polymerase Dpo4*♦ , 2007, Journal of Biological Chemistry.

[13]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[14]  L. A. Lipscomb,et al.  X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[15]  L. Prakash,et al.  Yeast DNA Polymerase ζ Is an Efficient Extender of Primer Ends Opposite from 7,8-Dihydro-8-Oxoguanine and O6-Methylguanine , 2003, Molecular and Cellular Biology.

[16]  Samuel H. Wilson,et al.  Magnesium-induced assembly of a complete DNA polymerase catalytic complex. , 2006, Structure.

[17]  C. Kisker,et al.  Lesion (in)tolerance reveals insights into DNA replication fidelity , 2004, The EMBO journal.

[18]  Samuel H. Wilson,et al.  Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. , 2008, Molecular cell.

[19]  Samuel H. Wilson,et al.  Metal-induced DNA translocation leads to DNA polymerase conformational activation , 2011, Nucleic acids research.

[20]  Robert E. Johnson,et al.  Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase η , 2000, Nature Genetics.

[21]  Robert E. Johnson,et al.  Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase η. , 2010, Structure.

[22]  J. Kraut,et al.  HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA , 1997 .

[23]  E. Ohtsuka,et al.  NMR studies of a DNA containing 8-hydroxydeoxyguanosine. , 1991, Nucleic acids research.

[24]  L. Beese,et al.  The Structure of a High Fidelity DNA Polymerase Bound to a Mismatched Nucleotide Reveals an “Ajar” Intermediate Conformation in the Nucleotide Selection Mechanism* , 2011, The Journal of Biological Chemistry.

[25]  References , 1971 .

[26]  Samuel H. Wilson,et al.  Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. , 2007, Biophysical journal.

[27]  M. Ikehara,et al.  Carbon-13 magnetic resonance spectra of 8-substituted purine nucleosides. Characteristic shifts for the syn conformation. , 1977, Journal of the American Chemical Society.

[28]  Samuel H. Wilson,et al.  Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. , 1997, Biochemistry.

[29]  Samuel H. Wilson,et al.  Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates. , 2004, The Journal of biological chemistry.

[30]  Yuan Cheng,et al.  Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion , 2006, PLoS biology.

[31]  Samuel H. Wilson,et al.  Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion , 2011, Proceedings of the National Academy of Sciences.

[32]  M. Egli,et al.  Structural and Functional Elucidation of the Mechanism Promoting Error-prone Synthesis by Human DNA Polymerase κ Opposite the 7,8-Dihydro-8-oxo-2′-deoxyguanosine Adduct* , 2009, The Journal of Biological Chemistry.

[33]  L. Prakash,et al.  Role of human DNA polymerase kappa as an extender in translesion synthesis. , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[35]  Samuel H. Wilson,et al.  DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine. , 2010, Mutation research.

[36]  Samuel H. Wilson,et al.  Structure and Mechanism of DNA Polymerase β , 2006, Biochemistry.

[37]  M. Washington,et al.  Mechanism of Efficient and Accurate Nucleotide Incorporation Opposite 7,8-Dihydro-8-Oxoguanine by Saccharomyces cerevisiae DNA Polymerase η , 2005, Molecular and Cellular Biology.

[38]  S. Doublié,et al.  Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69. , 2010, Biochemistry.

[39]  T. Carell,et al.  Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase , 2004, Nature.

[40]  G. Blackburn,et al.  The synthesis and metal binding characteristics of novel, isopolar phosphonate analogues of nucleotides , 1984 .

[41]  Samuel H. Wilson,et al.  Mutagenic conformation of 8-oxo-7,8-dihydro-2′-dGTP in the confines of a DNA polymerase active site , 2010, Nature Structural &Molecular Biology.

[42]  Jimin Wang,et al.  Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine . , 2010, Biochemistry.

[43]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[44]  F. Guengerich,et al.  Analysis of nucleotide insertion and extension at 8-oxo-7,8-dihydroguanine by replicative T7 polymerase exo- and human immunodeficiency virus-1 reverse transcriptase using steady-state and pre-steady-state kinetics. , 1997, Biochemistry.

[45]  Zucai Suo,et al.  Single-turnover Kinetic Analysis of the Mutagenic Potential of 8-Oxo-7,8-dihydro-2′-deoxyguanosine during Gap-filling Synthesis Catalyzed by Human DNA Polymerases λ and β , 2007 .

[46]  M. Egli,et al.  Efficient and High Fidelity Incorporation of dCTP Opposite 7,8-Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4* , 2005, Journal of Biological Chemistry.

[47]  Robert E. Johnson,et al.  Structure of Human DNA Polymerase κ Inserting dATP Opposite an 8-OxoG DNA Lesion , 2009, PloS one.

[48]  T. Kunkel,et al.  A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine. , 2005, Structure.

[49]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[50]  F. Guengerich,et al.  Fidelity of Nucleotide Insertion at 8-Oxo-7,8-dihydroguanine by Mammalian DNA Polymerase δ , 2001, The Journal of Biological Chemistry.

[51]  S. J. Culp,et al.  Structural and conformational analyses of 8-hydroxy-2'-deoxyguanosine. , 1989, Chemical research in toxicology.

[52]  Samuel H. Wilson,et al.  Efficiency of Correct Nucleotide Insertion Governs DNA Polymerase Fidelity* , 2002, The Journal of Biological Chemistry.

[53]  H. Ling,et al.  Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota , 2011, Proceedings of the National Academy of Sciences.

[54]  N. J. Gibson,et al.  Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs. , 1994, Biochemistry.

[55]  T. Kunkel,et al.  Structural basis for the dual coding potential of 8‐oxoguanosine by a high‐fidelity DNA polymerase , 2004, The EMBO journal.

[56]  L. Gold,et al.  Endogenous mutagens and the causes of aging and cancer. , 1991, Mutation research.