The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins

DNA polymerase zeta (pol z) participates in several DNA transactions in eukaryotic cells that increase spontaneous and damage-induced mutagenesis. To better understand this central role in mutagenesis in vivo, here we report the fidelity of DNA synthesis in vitro by yeast pol z alone and with RFC, PCNA and RPA. Overall, the accessory proteins have little effect on the fidelity of pol z. Pol z is relatively accurate for single base insertion/deletion errors. However, the average base substitution fidelity of pol z is substantially lower than that of homologous B family pols a, d and «. Pol z is particularly error prone for substitutions in specific sequence con-texts and generates multiple single base errors clustered in short patches at a rate that is unprece-dented in comparison with other polymerases. The unique error specificity of pol z in vitro is consistent with Pol z-dependent mutagenic specificity reported in vivo. This fact, combined with the high rate of single base substitution errors and complex muta-tions observed here, indicates that pol z contributes to mutagenesis in vivo not only by extending mismatches made by other polymerases, but also by directly generating its own mismatches and then extending them

Bismuth(III) Oxide Perchlorate Promoted Rearrangement of Epoxides to Aldehydes and Ketones

Aryl-substituted epoxides and aliphatic epoxides with a tertiary epoxide carbon undergo smooth rearrangement in the presence of 10–50 mol% bismuth(III) oxide perchlorate, BiOClO4•xH2O, to give carbonyl compounds. The rearrangement is regioselective with aryl substituted epoxides and a single carbonyl compound arising from cleavage of benzylic C―O bond is formed. BiOClO4•xH2O is relatively non-toxic, insensitive to air and inexpensive, making this catalyst an attractive alternative to more corrosive and toxic Lewis acids such as BF3•Et2O or InCl3 currently used to effect epoxide rearrangements

Idling by DNA polymerase δ maintains a ligatable nick during lagging-strand DNA replication

During each yeast cell cycle, ∼100,000 nicks are generated during lagging-strand DNA replication. Efficient nick processing during Okazaki fragment maturation requires the coordinated action of DNA polymerase δ (Pol δ) and the FLAP endonuclease FEN1. Misregulation of this process leads to the accumulation of double-stranded breaks and cell lethality. Our studies highlight a remarkably efficient mechanism for Okazaki fragment maturation in which Pol δ by default displaces 2–3 nt of any downstream RNA or DNA it encounters. In the presence of FEN1, efficient nick translation ensues, whereby a mixture of mono- and small oligonucleotides are released. If FEN1 is absent or not optimally functional, the ability of Pol δ to back up via its 3′–5′-exonuclease activity, a process called idling, maintains the polymerase at a position that is ideal either for ligation (in case of a DNA–DNA nick) or for subsequent engagement by FEN1 (in case of a DNA–RNA nick). Consistent with the hypothesis that DNA polymerase ε is the leading-strand enzyme, we observed no idling by this enzyme and no cooperation with FEN1 for creating a ligatable nick

The Multiple Biological Roles of the 3′→5′ Exonuclease of Saccharomyces cerevisiae DNA Polymerase δ Require Switching between the Polymerase and Exonuclease Domains

Until recently, the only biological function attributed to the 3′→5′ exonuclease activity of DNA polymerases was proofreading of replication errors. Based on genetic and biochemical analysis of the 3′→5′ exonuclease of yeast DNA polymerase δ (Pol δ) we have discerned additional biological roles for this exonuclease in Okazaki fragment maturation and mismatch repair. We asked whether Pol δ exonuclease performs all these biological functions in association with the replicative complex or as an exonuclease separate from the replicating holoenzyme. We have identified yeast Pol δ mutants at Leu523 that are defective in processive DNA synthesis when the rate of misincorporation is high because of a deoxynucleoside triphosphate (dNTP) imbalance. Yet the mutants retain robust 3′→5′ exonuclease activity. Based on biochemical studies, the mutant enzymes appear to be impaired in switching of the nascent 3′ end between the polymerase and the exonuclease sites, resulting in severely impaired biological functions. Mutation rates and spectra and synergistic interactions of the pol3-L523X mutations with msh2, exo1, and rad27/fen1 defects were indistinguishable from those observed with previously studied exonuclease-defective mutants of the Pol δ. We conclude that the three biological functions of the 3′→5′ exonuclease addressed in this study are performed intramolecularly within the replicating holoenzyme

A novel function of DNA polymerase ζ regulated by PCNA

DNA polymerase ζ (Polζ) participates in translesion DNA synthesis and is involved in the generation of the majority of mutations induced by DNA damage. The mechanisms that license access of Polζ to the primer terminus and regulate the extent of its participation in genome replication are poorly understood. The Polζ-dependent damage-induced mutagenesis requires monoubiquitination of proliferating cell nuclear antigen (PCNA) that is triggered by exposure to mutagens. We show that Polζ contributes to DNA replication and causes mutagenesis not only in response to DNA damage but also in response to malfunction of normal replicative machinery due to mutations in replication genes. These replication defects lead to ubiquitination of PCNA even in the absence of DNA damage. Unlike damage-induced mutagenesis, the Polζ-dependent spontaneous mutagenesis in replication mutants is reduced in strains defective in both ubiquitination and sumoylation of Lys164 of PCNA. Additionally, studies of a PCNA mutant defective for functional interactions with Polζ, but not for monoubiquitination by the Rad6/Rad18 complex demonstrate a role for PCNA in regulating the mutagenic activity of Polζ separate from its modification at Lys164