Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase

Nucleic Acids Res. 2013 Feb 1;41(3):2060-71. doi: 10.1093/nar/gks1296. Epub 2012 Dec 24.

Abstract

Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyrene-derived DNA lesions generates mutations that likely play a role in the etiology of cancer. Here, we report two crystal structures of the human Y-family DNA polymerase iota complexed with the major 1-nitropyrene DNA lesion at the insertion stage, incorporating either dCTP or dATP nucleotide opposite the lesion. Polι maintains the adduct in its active site in two distinct conformations. dCTP forms a Watson-Crick base pair with the adducted guanine and excludes the pyrene ring from the helical DNA, which inhibits replication beyond the lesion. By contrast, the mismatched dATP stacks above the pyrene ring that is intercalated in the helix and achieves a productive conformation for misincorporation. The intra-helical bulky pyrene mimics a base pair in the active site and facilitates adenine misincorporation. By structure-based mutagenesis, we show that the restrictive active site of human polη prevents the intra-helical conformation and A-base misinsertions. This work provides one of the molecular mechanisms for G to T transversions, a signature mutation in human lung cancer.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carcinogens / chemistry*
  • DNA Adducts / chemistry*
  • DNA Polymerase iota
  • DNA Replication
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism
  • Deoxyadenine Nucleotides / chemistry
  • Deoxyadenine Nucleotides / metabolism
  • Deoxycytosine Nucleotides / chemistry
  • Deoxycytosine Nucleotides / metabolism
  • Deoxyguanosine / analogs & derivatives*
  • Deoxyguanosine / chemistry
  • Humans
  • Models, Molecular
  • Pyrenes / chemistry*

Substances

  • Carcinogens
  • DNA Adducts
  • Deoxyadenine Nucleotides
  • Deoxycytosine Nucleotides
  • N-(deoxyguanosine-8-yl)-1-aminopyrene
  • Pyrenes
  • 2'-deoxycytidine 5'-triphosphate
  • DNA-Directed DNA Polymerase
  • Rad30 protein
  • Deoxyguanosine
  • 2'-deoxyadenosine triphosphate
  • DNA Polymerase iota
  • POLI protein, human

Associated data

  • PDB/4EYH
  • PDB/4EYI