Localization of the phosphoester bond hydrolyzed by the major apurinic/apyrmidinic endodeoxyribonuclease from rat-liver chromatin

Nucleotide excision repair of abasic DNA lesions

Apurinic/apyrimidinic (AP) sites are a class of highly mutagenic and toxic DNA lesions arising in the genome from a number of exogenous and endogenous sources. Repair of AP lesions takes place predominantly by the base excision pathway (BER). However, among chemically heterogeneous AP lesions formed in DNA, some are resistant to the endonuclease APE1 and thus refractory to BER. Here, we employed two types of reporter constructs accommodating synthetic APE1-resistant AP lesions to investigate the auxiliary repair mechanisms in human cells. By combined analyses of recovery of the transcription rate and suppression of transcriptional mutagenesis at specifically positioned AP lesions, we demonstrate that nucleotide excision repair pathway (NER) efficiently removes BER-resistant AP lesions and significantly enhances the repair of APE1-sensitive ones. Our results further indicate that core NER components XPA and XPF are equally required and that both global genome (GG-NER) and transcription coupled (TC-NER) subpathways contribute to the repair.

An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro

The Kae1 (Kinase-associated endopeptidase 1) protein is a member of the recently identified transcription complex EKC and telomeres maintenance complex KEOPS in yeast. Kae1 homologues are encoded by all sequenced genomes in the three domains of life. Although annotated as putative endopeptidases, the actual functions of these universal proteins are unknown. Here we show that the purified Kae1 protein (Pa-Kae1) from Pyrococcus abyssi is an iron-protein with a novel type of ATP-binding site. Surprisingly, this protein did not exhibit endopeptidase activity in vitro but binds cooperatively to single and double-stranded DNA and induces unusual DNA conformational change. Furthermore, Pa-Kae1 exhibits a class I apurinic (AP)-endonuclease activity (AP-lyase). Both DNA binding and AP-endonuclease activity are inhibited by ATP. Kae1 is thus a novel and atypical universal DNA interacting protein whose importance could rival those of RecA (RadA/Rad51) in the maintenance of genome integrity in all living cells.

The enzymology of apurinic/apyrimidinic endonucleases

Studies on the enzymology of apurinic/apyrimidinic (AP) endonucleases from procaryotic and eucaryotic organisms are reviewed. Emphasis will be placed on the enzymes from Escherichia coli from which a considerable portion of our knowledge has been derived. Recent studies on similar enzymes from eucaryotes will be discussed as well. In addition, we will discuss the chemical and physical properties of AP sites and review studies on peptides and acridine derivatives which incise DNA at AP sites.

The apurinic/apyrimidinic endodeoxyribonuclease of rat-liver chromatin

The extract from rat liver chromatin contains two apurinic/apyrimidinic (AP) endodeoxyribonucleases named 0.2 M and 0.3 M isozymes according to the phosphate concentration necessary to elute them from an hydroxyapatite column. The 0.3 M isozyme is the main and perhaps the only chromatin AP endodeoxyribonuclease in the living cell. This 0.3 M isozyme was purified by successive chromatographies on hydroxyapatite, phosphocellulose, heparin-Sepharose and alkylated-depurinated DNA-cellulose. It has a molecular weight of approximately 39000; its optimum pH is around 8.0; it needs Mg2+ or Mn2+ to be active and the optimum concentration for Mg2+ is between 5 mM and 10 mM. The 0.3 M isozyme has no action on intact DNA strands or on alkylated sites; it cuts the phosphodiester bridge which is the immediate neighbour of the AP site on its 5' side leaving 3'-hydroxyl and 5'-phosphate ends. It has no associated exonuclease activity. To hydrolyze the phosphoester bond near the AP site, the enzyme makes a close contact with three base residues in the large groove of the DNA molecule.

Repair of AP sites in DNA

Escherichia coli endonuclease VI is a deoxyribonuclease specific for AP (apurinic or apyrimidinic) sites; it cleaves the phosphodiester bond immediately neighbouring the AP site on its 5' side leaving 3'-hydroxyl and 5'-phosphate ends. DNA with AP sites can be repaired in vitro with endonuclease VI, DNA polymerase I and ligase; the repair mechanism is described. E. coli has other AP endonucleases; some of them are not specific for AP sites and some of them cut 3' to the AP sites. Most of the rat liver AP endonuclease activity is in chromatin. Some is however found in other cell compartments and it has been speculated that these enzymes might be precursors of the chromatin enzyme. The chromatin AP endonuclease is specific for AP sites; it cuts 5' to the AP site. DNA with AP sites can be repaired in vitro with enzymes purified from chromatin; AP endonuclease, 5'-3 exonuclease, DNA polymerase beta and ligase.