Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the sulfolobus solfataricus DNA polymerase Dpo4

Ganesh Shanmugam, Irina Minko, Surajit Banerjee, Plamen P. Christov, Ivan D. Kozekov, Carmelo J. Rizzo, Robert (Stephen) Lloyd, Martin Egli, Michael P. Stone

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Acrolein, a mutagenic aldehyde, reacts with deoxyguanosine (dG) to form 3-(2′-deoxy-β-d-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8- hydroxypyrimido[1,2-a] purin-10(3H)-one (γ-OH-PdG). When placed opposite deoxycytosine (dC) in DNA, γ-OH-PdG undergoes ring-opening to the N 2-(3-oxopropyl)-dG. Ring-opening of the adduct has been hypothesized to facilitate nonmutagenic bypass, particularly by DNA polymerases of the Y family. This study examined the bypass of γ-OH-PdG by Sulfolobus solfataricus Dpo4, the prototypic Y-family DNA polymerase, using templates that contained the adduct in either the 5′-CXG-3′ or the 5′-TXG-3′ sequence context. Although γ-OH-PdG partially blocked Dpo4-catalyzed DNA synthesis, full primer extension was observed, and the majority of bypass products were error-free. Conversion of the adduct into an irreversibly ring-opened derivative prior to reaction facilitated bypass and further improved the fidelity. Structures of ternary Dpo4·DNA·dNTP complexes were determined with primers that either were positioned immediately upstream of the lesion (preinsertion complexes) or had a 3′-terminal dC opposite the lesion (postinsertion complexes); the incoming nucleotides, either dGTP or dATP, were complementary to the template 5′-neighbor nucleotide. In both postinsertion complexes, the adduct existed as ring-opened species, and the resulting base-pair featured Watson-Crick hydrogen bonding. The incoming nucleotide paired with the 5′-neighbor template, while the primer 3′-hydroxyl was positioned to facilitate extension. In contrast, γ-OH-PdG was in the ring-closed form in both preinsertion complexes, and the overall structure did not favor catalysis. These data provide insights into γ-OH-PdG chemistry during replication bypass by the Dpo4 DNA polymerase and may explain why γ-OH-PdG-induced mutations due to primer-template misalignment are uncommon.

Original languageEnglish (US)
Pages (from-to)1348-1360
Number of pages13
JournalChemical Research in Toxicology
Volume26
Issue number9
DOIs
StatePublished - Sep 16 2013

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Sulfolobus solfataricus
DNA-Directed DNA Polymerase
Deoxyguanosine
Nucleotides
Acrolein
DNA
Hydrogen Bonding
hydroxide ion
Catalysis
Aldehydes
Base Pairing
Hydroxyl Radical
Hydrogen bonds
Derivatives
Mutation

ASJC Scopus subject areas

  • Toxicology

Cite this

Shanmugam, G., Minko, I., Banerjee, S., Christov, P. P., Kozekov, I. D., Rizzo, C. J., ... Stone, M. P. (2013). Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the sulfolobus solfataricus DNA polymerase Dpo4. Chemical Research in Toxicology, 26(9), 1348-1360. https://doi.org/10.1021/tx400200b

Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the sulfolobus solfataricus DNA polymerase Dpo4. / Shanmugam, Ganesh; Minko, Irina; Banerjee, Surajit; Christov, Plamen P.; Kozekov, Ivan D.; Rizzo, Carmelo J.; Lloyd, Robert (Stephen); Egli, Martin; Stone, Michael P.

In: Chemical Research in Toxicology, Vol. 26, No. 9, 16.09.2013, p. 1348-1360.

Research output: Contribution to journalArticle

Shanmugam, G, Minko, I, Banerjee, S, Christov, PP, Kozekov, ID, Rizzo, CJ, Lloyd, RS, Egli, M & Stone, MP 2013, 'Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the sulfolobus solfataricus DNA polymerase Dpo4', Chemical Research in Toxicology, vol. 26, no. 9, pp. 1348-1360. https://doi.org/10.1021/tx400200b
Shanmugam, Ganesh ; Minko, Irina ; Banerjee, Surajit ; Christov, Plamen P. ; Kozekov, Ivan D. ; Rizzo, Carmelo J. ; Lloyd, Robert (Stephen) ; Egli, Martin ; Stone, Michael P. / Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the sulfolobus solfataricus DNA polymerase Dpo4. In: Chemical Research in Toxicology. 2013 ; Vol. 26, No. 9. pp. 1348-1360.
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abstract = "Acrolein, a mutagenic aldehyde, reacts with deoxyguanosine (dG) to form 3-(2′-deoxy-β-d-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8- hydroxypyrimido[1,2-a] purin-10(3H)-one (γ-OH-PdG). When placed opposite deoxycytosine (dC) in DNA, γ-OH-PdG undergoes ring-opening to the N 2-(3-oxopropyl)-dG. Ring-opening of the adduct has been hypothesized to facilitate nonmutagenic bypass, particularly by DNA polymerases of the Y family. This study examined the bypass of γ-OH-PdG by Sulfolobus solfataricus Dpo4, the prototypic Y-family DNA polymerase, using templates that contained the adduct in either the 5′-CXG-3′ or the 5′-TXG-3′ sequence context. Although γ-OH-PdG partially blocked Dpo4-catalyzed DNA synthesis, full primer extension was observed, and the majority of bypass products were error-free. Conversion of the adduct into an irreversibly ring-opened derivative prior to reaction facilitated bypass and further improved the fidelity. Structures of ternary Dpo4·DNA·dNTP complexes were determined with primers that either were positioned immediately upstream of the lesion (preinsertion complexes) or had a 3′-terminal dC opposite the lesion (postinsertion complexes); the incoming nucleotides, either dGTP or dATP, were complementary to the template 5′-neighbor nucleotide. In both postinsertion complexes, the adduct existed as ring-opened species, and the resulting base-pair featured Watson-Crick hydrogen bonding. The incoming nucleotide paired with the 5′-neighbor template, while the primer 3′-hydroxyl was positioned to facilitate extension. In contrast, γ-OH-PdG was in the ring-closed form in both preinsertion complexes, and the overall structure did not favor catalysis. These data provide insights into γ-OH-PdG chemistry during replication bypass by the Dpo4 DNA polymerase and may explain why γ-OH-PdG-induced mutations due to primer-template misalignment are uncommon.",
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AU - Kozekov, Ivan D.

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N2 - Acrolein, a mutagenic aldehyde, reacts with deoxyguanosine (dG) to form 3-(2′-deoxy-β-d-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8- hydroxypyrimido[1,2-a] purin-10(3H)-one (γ-OH-PdG). When placed opposite deoxycytosine (dC) in DNA, γ-OH-PdG undergoes ring-opening to the N 2-(3-oxopropyl)-dG. Ring-opening of the adduct has been hypothesized to facilitate nonmutagenic bypass, particularly by DNA polymerases of the Y family. This study examined the bypass of γ-OH-PdG by Sulfolobus solfataricus Dpo4, the prototypic Y-family DNA polymerase, using templates that contained the adduct in either the 5′-CXG-3′ or the 5′-TXG-3′ sequence context. Although γ-OH-PdG partially blocked Dpo4-catalyzed DNA synthesis, full primer extension was observed, and the majority of bypass products were error-free. Conversion of the adduct into an irreversibly ring-opened derivative prior to reaction facilitated bypass and further improved the fidelity. Structures of ternary Dpo4·DNA·dNTP complexes were determined with primers that either were positioned immediately upstream of the lesion (preinsertion complexes) or had a 3′-terminal dC opposite the lesion (postinsertion complexes); the incoming nucleotides, either dGTP or dATP, were complementary to the template 5′-neighbor nucleotide. In both postinsertion complexes, the adduct existed as ring-opened species, and the resulting base-pair featured Watson-Crick hydrogen bonding. The incoming nucleotide paired with the 5′-neighbor template, while the primer 3′-hydroxyl was positioned to facilitate extension. In contrast, γ-OH-PdG was in the ring-closed form in both preinsertion complexes, and the overall structure did not favor catalysis. These data provide insights into γ-OH-PdG chemistry during replication bypass by the Dpo4 DNA polymerase and may explain why γ-OH-PdG-induced mutations due to primer-template misalignment are uncommon.

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