title: Intrinsic properties of the two replicative DNA polymerases of Pyrococcus abyssi in replicating abasic sites: possible role in DNA damage tolerance?
abstract: Spontaneous and induced abasic sites in hyperthermophiles DNA have long been suspected to occur at high frequency. Here, Pyrococcus abyssi was used as an attractive model to analyse the impact of such lesions onto the maintenance of genome integrity. We demonstrated that endogenous AP sites persist at a slightly higher level in P. abyssi genome compared with Escherichia coli. Then, the two replicative DNA polymerases, PabpolB and PabpolD, were characterized in presence of DNA containing abasic sites. Both Pabpols had abortive DNA synthesis upon encountering AP sites. Under running start conditions, PabpolB could incorporate in front of the damage and even replicate to the full-length oligonucleotides containing a specific AP site, but only when present at a molar excess. Conversely, bypassing activity of PabpolD was strictly inhibited. The tight regulation of nucleotide incorporation opposite the AP site was assigned to the efficiency of the proof-reading function, because exonuclease-deficient enzymes exhibited effective TLS. Steady-state kinetics reinforced that Pabpols are high-fidelity DNA polymerases onto undamaged DNA. Moreover, Pabpols preferentially inserted dAMP opposite an AP site, albeit inefficiently. While the template sequence of the oligonucleotides did not influence the nucleotide insertion, the DNA topology could impact on the progression of Pabpols. Our results are interpreted in terms of DNA damage tolerance.
authors.affiliation: Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, BP 70, 29280 Plouzané, France.
authors.forename: Adeline
authors.initials: A
authors.lastname: Palud
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Villani
authors.forename: Stéphane
authors.initials: S
authors.lastname: L'Haridon
authors.forename: Joël
authors.initials: J
authors.lastname: Querellou
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Raffin
authors.forename: Ghislaine
authors.initials: G
authors.lastname: Henneke
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D004249:DNA Damage; D004261:DNA Replication; D019641:DNA, Archaeal / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004270:DNA, Circular / Q000235:genetics; D004259:DNA-Directed DNA Polymerase / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005092:Exonucleases / Q000235:genetics / Q000378:metabolism; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D007700:Kinetics; D008969:Molecular Sequence Data; D009154:Mutation; D009711:Nucleotides / Q000378:metabolism; D043903:Pyrococcus abyssi / Q000235:genetics* / Q000378:metabolism; D013698:Templates, Genetic
chemical_list: D019843:Archaeal Proteins; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004270:DNA, Circular; D009711:Nucleotides; D004259:DNA-Directed DNA Polymerase; D005092:Exonucleases