Cell Reports (Oct 2022)

Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2

  • Jessica S. Williams,
  • Jessica L. Wojtaszek,
  • Denise C. Appel,
  • Juno Krahn,
  • Bret D. Wallace,
  • Evan Walsh,
  • Thomas A. Kunkel,
  • R. Scott Williams

Journal volume & issue
Vol. 41, no. 1
p. 111448

Abstract

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Summary: Topoisomerase 1 (Top1) incises DNA containing ribonucleotides to generate complex DNA lesions that are resolved by APE2 (Apn2 in yeast). How Apn2 engages and processes this DNA damage is unclear. Here, we report X-ray crystal structures and biochemical analysis of Apn2-DNA complexes to demonstrate how Apn2 frays and cleaves 3′ DNA termini via a wedging mechanism that facilitates 1–6 nucleotide endonucleolytic cleavages. APN2 deletion and DNA-wedge mutant Saccharomyces cerevisiae strains display mutator phenotypes, cell growth defects, and sensitivity to genotoxic stress in a ribonucleotide excision repair (RER)-defective background harboring a high density of Top1-incised ribonucleotides. Our data implicate a wedge-and-cut mechanism underpinning the broad-specificity Apn2 nuclease activity that mitigates mutagenic and genome instability phenotypes caused by Top1 incision at genomic ribonucleotides incorporated by DNA polymerase epsilon.

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